Should I use LaTeX or Word for my thesis?

LaTeX is generally better for theses, especially in STEM fields. It handles long documents with hundreds of pages without performance issues, automatically manages cross-references and citations, and produces professional typography. The initial learning curve pays off for documents of thesis length.

Where can I find a LaTeX thesis template for my university?

Check your graduate school or department website first, as most universities provide official templates. You can also search for your university name plus thesis template LaTeX. If no official template exists, start with a standard report class and adapt it to your requirements.

How should I organize the files for a thesis in LaTeX?

Use a main.tex file that includes separate files for each chapter. Keep figures in a dedicated folder organized by chapter. Store your bibliography in a single .bib file. This structure makes it easier to compile individual chapters during writing and keeps the project manageable.

Why do I need to run LaTeX multiple times to get correct references?

LaTeX uses a multi-pass system. The first pass identifies labels and citations, writing them to auxiliary files. BibTeX then processes citations. Subsequent LaTeX passes read these files to resolve cross-references. Three passes after BibTeX usually resolves everything.

Write Your Thesis in LaTeX: The Complete PhD Survival Guide

The 3 AM Formatting Nightmare

It's 3 AM. Your thesis defense is in two weeks. You just added a figure to Chapter 3, and now every figure number after it is wrong. The table of contents is broken. Word is freezing every time you scroll. You're considering switching to interpretive dance as your dissertation format.

This doesn't have to be your story.

Every year, thousands of PhD students discover LaTeX halfway through their thesis—and kick themselves for not starting sooner. LaTeX handles 200-page documents with hundreds of references like it was designed for them. Because it was.

This guide gives you everything: file organization, templates, cross-references, bibliographies, and the tricks that experienced thesis writers wish someone had told them.

Before You Start

Get the Right Template

Most universities provide official LaTeX thesis templates. Start there:

Check your graduate school website
Ask your department administrator
Search for your university + "thesis template LaTeX"

These templates handle:

Title page formatting
Margin requirements
Front matter structure
Chapter heading styles
Bibliography format

Starting with the official template saves hours of formatting work. You can also browse our thesis template gallery for professionally designed options.

Organize Your Files

A thesis has many files. Organize from day one:

thesis/
├── main.tex              # Master document
├── preamble.tex          # Packages and settings
├── frontmatter/
│   ├── abstract.tex
│   ├── acknowledgments.tex
│   └── dedication.tex
├── chapters/
│   ├── introduction.tex
│   ├── literature.tex
│   ├── methods.tex
│   ├── results.tex
│   └── conclusion.tex
├── appendices/
│   ├── appendix-a.tex
│   └── appendix-b.tex
├── figures/
│   ├── chapter-3/
│   └── chapter-4/
├── references.bib
└── thesis.cls             # Custom class (if any)

Document Structure

The Master Document

Your main.tex file is the conductor:

\documentclass[12pt, oneside]{report}
 
\input{preamble}
 
\begin{document}
 
% Front matter
\frontmatter
\input{frontmatter/titlepage}
\input{frontmatter/abstract}
\input{frontmatter/acknowledgments}
\tableofcontents
\listoffigures
\listoftables
 
% Main content
\mainmatter
\input{chapters/introduction}
\input{chapters/literature}
\input{chapters/methods}
\input{chapters/results}
\input{chapters/conclusion}
 
% Back matter
\backmatter
\input{appendices/appendix-a}
\bibliography{references}
 
\end{document}

Front Matter

Front matter includes everything before Chapter 1:

% Title page (often specific format required)
\begin{titlepage}
\centering
\vspace*{2cm}
{\Huge\bfseries Your Thesis Title\par}
\vspace{1cm}
{\Large by\par}
{\Large Your Name\par}
\vspace{2cm}
{\large A thesis submitted in partial fulfillment...}
\end{titlepage}
 
% Abstract
\chapter*{Abstract}
\addcontentsline{toc}{chapter}{Abstract}
Your abstract text here...
 
% Acknowledgments
\chapter*{Acknowledgments}
\addcontentsline{toc}{chapter}{Acknowledgments}
Thanks to...

Chapters

Each chapter is a separate file:

% chapters/introduction.tex
\chapter{Introduction}
\label{ch:introduction}
 
\section{Background}
\label{sec:intro-background}
 
Your research addresses a critical gap in...
 
\section{Research Questions}
\label{sec:intro-questions}
 
This thesis investigates three primary questions:
 
\begin{enumerate}
    \item How does X affect Y?
    \item What is the relationship between...
    \item Can we predict...
\end{enumerate}
 
\section{Thesis Structure}
\label{sec:intro-structure}
 
Chapter \ref{ch:literature} reviews existing work...
Chapter \ref{ch:methods} describes the methodology...

Essential Packages

The Preamble

Keep package declarations organized:

% preamble.tex
 
% Document setup
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage[english]{babel}
 
% Page layout
\usepackage[margin=1in]{geometry}
\usepackage{setspace}
\doublespacing
 
% Math
\usepackage{amsmath, amssymb, amsthm}
 
% Figures and tables
\usepackage{graphicx}
\usepackage{booktabs}
\usepackage{float}
\usepackage{subcaption}
 
% Bibliography
\usepackage[round]{natbib}
 
% References and links
\usepackage{hyperref}
\usepackage{cleveref}
 
% Code listings (if needed)
\usepackage{listings}
 
% Custom commands
\newcommand{\thesis}{\textit{Thesis Title}}

Package Recommendations

| Need | Package | |------|---------| | Margins | geometry | | Line spacing | setspace | | Better tables | booktabs | | Subfigures | subcaption | | Smart references | cleveref | | URLs | url or hyperref | | Code | listings or minted |

Figures and Tables

Figure Organization

Keep figures organized by chapter:

\graphicspath{
    {figures/}
    {figures/chapter-3/}
    {figures/chapter-4/}
}
 
% Then in your chapters:
\begin{figure}[htbp]
    \centering
    \includegraphics[width=0.8\textwidth]{results-graph}
    \caption{Experimental results showing...}
    \label{fig:results-graph}
\end{figure}

Subfigures

For multi-panel figures:

\usepackage{subcaption}
 
\begin{figure}[htbp]
    \centering
    \begin{subfigure}[b]{0.45\textwidth}
        \includegraphics[width=\textwidth]{control-group}
        \caption{Control group}
        \label{fig:control}
    \end{subfigure}
    \hfill
    \begin{subfigure}[b]{0.45\textwidth}
        \includegraphics[width=\textwidth]{treatment-group}
        \caption{Treatment group}
        \label{fig:treatment}
    \end{subfigure}
    \caption{Comparison of control and treatment groups.}
    \label{fig:comparison}
\end{figure}

Tables

Use booktabs for professional tables (or use our table generator to create them visually):

\begin{table}[htbp]
    \centering
    \caption{Summary of experimental conditions}
    \label{tab:conditions}
    \begin{tabular}{lccc}
        \toprule
        Condition & Temperature & Duration & Samples \\
        \midrule
        A & 25°C & 24h & 50 \\
        B & 37°C & 24h & 50 \\
        C & 25°C & 48h & 50 \\
        D & 37°C & 48h & 50 \\
        \bottomrule
    \end{tabular}
\end{table}

Bibliography Management

BibTeX Basics

Maintain your .bib file throughout your PhD, not just when writing:

@article{smith2020,
    author  = {Smith, John and Doe, Jane},
    title   = {A Revolutionary Finding},
    journal = {Journal of Important Science},
    year    = {2020},
    volume  = {42},
    pages   = {1--15},
    doi     = {10.1234/jis.2020.001}
}

Citation Commands

With natbib:

\citet{smith2020} found that...     % Smith and Doe (2020) found...
According to \citet{smith2020}...   % According to Smith and Doe (2020)...
Previous work \citep{smith2020}...  % Previous work (Smith and Doe, 2020)...

Bibliography Style

Use the style required by your university:

\bibliographystyle{apalike}  % or whatever your school requires
\bibliography{references}

Cross-References

Labels

Label everything you might reference:

\chapter{Methods}
\label{ch:methods}
 
\section{Data Collection}
\label{sec:data-collection}
 
As shown in Figure \ref{fig:apparatus}...
Table \ref{tab:results} summarizes...
This is discussed further in Section \ref{sec:discussion}.

Smart References with cleveref

The cleveref package automates reference formatting:

\usepackage{cleveref}
 
\Cref{ch:methods} describes...     % Chapter 3 describes...
As shown in \cref{fig:results}...  % As shown in Figure 4.2...
See \cref{tab:a,tab:b,tab:c}...    % See Tables 2.1, 2.2, and 2.3...

Managing Long Documents

Compiling Chapters Individually

For faster compilation during writing:

% At the start of main.tex:
\includeonly{chapters/methods}
 
% Your \include statements:
\include{chapters/introduction}
\include{chapters/literature}
\include{chapters/methods}      % Only this compiles
\include{chapters/results}
\include{chapters/conclusion}

Comment out \includeonly for the full document.

Draft Mode

Speed up compilation during writing:

\documentclass[12pt, draft]{report}

Draft mode:

Shows overfull/underfull box warnings
Replaces images with placeholders
Compiles faster

Compile Workflow

For the final document:

pdflatex main
bibtex main
pdflatex main
pdflatex main

Yes, run LaTeX three times for all references to resolve.

Thesis-Specific Tips

Consistent Terminology

Define terms once:

% In preamble
\newcommand{\myterm}{Specific Technical Term}
\newcommand{\mytool}{\textsc{ToolName}}
 
% In text
We used \mytool{} to analyze \myterm{} data.

TODO Notes

Track what needs work:

\usepackage[colorinlistoftodos]{todonotes}
 
\todo{Need to add more citations here}
\todo[inline]{Rewrite this section}
\missingfigure{Chart showing results}
 
% Get a list of all todos:
\listoftodos

Revision Tracking

For advisor feedback:

\usepackage{changes}
 
\added{New text added}
\deleted{Text removed}
\replaced{new text}{old text}
 
% Or simpler highlighting:
\usepackage{soul}
\hl{Highlighted text for review}

Common Thesis Problems

Overfull Boxes

Overfull \hbox (12.3pt too wide)

The text extends past the margin. Solutions:

Let LaTeX break the word: \hyphenation{prob-lem-at-ic}
Force line break: \\
Allow slight margin overflow: \sloppy (last resort)

Figure Placement

Figures floating to wrong locations:

% Force figure here
\begin{figure}[H]  % Requires float package
 
% Or adjust float parameters
\renewcommand{\topfraction}{0.9}
\renewcommand{\bottomfraction}{0.9}
\renewcommand{\textfraction}{0.1}

Bibliography Not Appearing

Ensure you cite at least one source
Run BibTeX after LaTeX
Check .bib file is in the right location
Verify \bibliography{} points to correct file (without .bib extension)

Pre-Submission Checklist

Before submitting:

[ ] All chapters compile without errors
[ ] All references resolve (no ??)
[ ] All citations exist (no missing references)
[ ] Page numbers are correct
[ ] Table of contents is up to date
[ ] List of figures/tables is complete
[ ] Bibliography is complete and formatted correctly
[ ] Margins meet requirements
[ ] Line spacing meets requirements
[ ] Figure quality is sufficient for printing
[ ] PDF is searchable (not scanned images)

Backup Strategy

A thesis represents years of work. Protect it:

Version control: Use Git for all files
Cloud backup: Sync to cloud storage
Multiple locations: Keep copies in different places
Regular commits: Commit after each writing session

git init
git add .
git commit -m "Initial thesis structure"
# ... work ...
git commit -m "Completed methods chapter first draft"

Conclusion

Writing a thesis in LaTeX takes effort to learn, but pays dividends:

Consistent formatting throughout
Reliable cross-references
Professional typography
Easy bibliography management
Handles 100+ pages without problems

Start with your university's template, organize your files well, and build your document incrementally. By the time you're done, you'll have a professional document you're proud to submit.

The thesis itself is hard enough. Let LaTeX handle the formatting so you can focus on the research.

The 3 AM Formatting Nightmare

This doesn't have to be your story.

This guide gives you everything: file organization, templates, cross-references, bibliographies, and the tricks that experienced thesis writers wish someone had told them.

Before You Start

Get the Right Template

Most universities provide official LaTeX thesis templates. Start there:

Check your graduate school website
Ask your department administrator
Search for your university + "thesis template LaTeX"

These templates handle:

Title page formatting
Margin requirements
Front matter structure
Chapter heading styles
Bibliography format

Starting with the official template saves hours of formatting work. You can also browse our thesis template gallery for professionally designed options.

Organize Your Files

A thesis has many files. Organize from day one:

thesis/
├── main.tex              # Master document
├── preamble.tex          # Packages and settings
├── frontmatter/
│   ├── abstract.tex
│   ├── acknowledgments.tex
│   └── dedication.tex
├── chapters/
│   ├── introduction.tex
│   ├── literature.tex
│   ├── methods.tex
│   ├── results.tex
│   └── conclusion.tex
├── appendices/
│   ├── appendix-a.tex
│   └── appendix-b.tex
├── figures/
│   ├── chapter-3/
│   └── chapter-4/
├── references.bib
└── thesis.cls             # Custom class (if any)

Document Structure

The Master Document

Your main.tex file is the conductor:

\documentclass[12pt, oneside]{report}
 
\input{preamble}
 
\begin{document}
 
% Front matter
\frontmatter
\input{frontmatter/titlepage}
\input{frontmatter/abstract}
\input{frontmatter/acknowledgments}
\tableofcontents
\listoffigures
\listoftables
 
% Main content
\mainmatter
\input{chapters/introduction}
\input{chapters/literature}
\input{chapters/methods}
\input{chapters/results}
\input{chapters/conclusion}
 
% Back matter
\backmatter
\input{appendices/appendix-a}
\bibliography{references}
 
\end{document}

Front Matter

Front matter includes everything before Chapter 1:

% Title page (often specific format required)
\begin{titlepage}
\centering
\vspace*{2cm}
{\Huge\bfseries Your Thesis Title\par}
\vspace{1cm}
{\Large by\par}
{\Large Your Name\par}
\vspace{2cm}
{\large A thesis submitted in partial fulfillment...}
\end{titlepage}
 
% Abstract
\chapter*{Abstract}
\addcontentsline{toc}{chapter}{Abstract}
Your abstract text here...
 
% Acknowledgments
\chapter*{Acknowledgments}
\addcontentsline{toc}{chapter}{Acknowledgments}
Thanks to...

Chapters

Each chapter is a separate file:

% chapters/introduction.tex
\chapter{Introduction}
\label{ch:introduction}
 
\section{Background}
\label{sec:intro-background}
 
Your research addresses a critical gap in...
 
\section{Research Questions}
\label{sec:intro-questions}
 
This thesis investigates three primary questions:
 
\begin{enumerate}
    \item How does X affect Y?
    \item What is the relationship between...
    \item Can we predict...
\end{enumerate}
 
\section{Thesis Structure}
\label{sec:intro-structure}
 
Chapter \ref{ch:literature} reviews existing work...
Chapter \ref{ch:methods} describes the methodology...

Essential Packages

The Preamble

Keep package declarations organized:

% preamble.tex
 
% Document setup
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage[english]{babel}
 
% Page layout
\usepackage[margin=1in]{geometry}
\usepackage{setspace}
\doublespacing
 
% Math
\usepackage{amsmath, amssymb, amsthm}
 
% Figures and tables
\usepackage{graphicx}
\usepackage{booktabs}
\usepackage{float}
\usepackage{subcaption}
 
% Bibliography
\usepackage[round]{natbib}
 
% References and links
\usepackage{hyperref}
\usepackage{cleveref}
 
% Code listings (if needed)
\usepackage{listings}
 
% Custom commands
\newcommand{\thesis}{\textit{Thesis Title}}

Package Recommendations

Figures and Tables

Figure Organization

Keep figures organized by chapter:

\graphicspath{
    {figures/}
    {figures/chapter-3/}
    {figures/chapter-4/}
}
 
% Then in your chapters:
\begin{figure}[htbp]
    \centering
    \includegraphics[width=0.8\textwidth]{results-graph}
    \caption{Experimental results showing...}
    \label{fig:results-graph}
\end{figure}

Subfigures

For multi-panel figures:

\usepackage{subcaption}
 
\begin{figure}[htbp]
    \centering
    \begin{subfigure}[b]{0.45\textwidth}
        \includegraphics[width=\textwidth]{control-group}
        \caption{Control group}
        \label{fig:control}
    \end{subfigure}
    \hfill
    \begin{subfigure}[b]{0.45\textwidth}
        \includegraphics[width=\textwidth]{treatment-group}
        \caption{Treatment group}
        \label{fig:treatment}
    \end{subfigure}
    \caption{Comparison of control and treatment groups.}
    \label{fig:comparison}
\end{figure}

Tables

Use booktabs for professional tables (or use our table generator to create them visually):

\begin{table}[htbp]
    \centering
    \caption{Summary of experimental conditions}
    \label{tab:conditions}
    \begin{tabular}{lccc}
        \toprule
        Condition & Temperature & Duration & Samples \\
        \midrule
        A & 25°C & 24h & 50 \\
        B & 37°C & 24h & 50 \\
        C & 25°C & 48h & 50 \\
        D & 37°C & 48h & 50 \\
        \bottomrule
    \end{tabular}
\end{table}

Bibliography Management

BibTeX Basics

Maintain your .bib file throughout your PhD, not just when writing:

@article{smith2020,
    author  = {Smith, John and Doe, Jane},
    title   = {A Revolutionary Finding},
    journal = {Journal of Important Science},
    year    = {2020},
    volume  = {42},
    pages   = {1--15},
    doi     = {10.1234/jis.2020.001}
}

Citation Commands

With natbib:

\citet{smith2020} found that...     % Smith and Doe (2020) found...
According to \citet{smith2020}...   % According to Smith and Doe (2020)...
Previous work \citep{smith2020}...  % Previous work (Smith and Doe, 2020)...

Bibliography Style

Use the style required by your university:

\bibliographystyle{apalike}  % or whatever your school requires
\bibliography{references}

Cross-References

Labels

Label everything you might reference:

\chapter{Methods}
\label{ch:methods}
 
\section{Data Collection}
\label{sec:data-collection}
 
As shown in Figure \ref{fig:apparatus}...
Table \ref{tab:results} summarizes...
This is discussed further in Section \ref{sec:discussion}.

Smart References with cleveref

The cleveref package automates reference formatting:

\usepackage{cleveref}
 
\Cref{ch:methods} describes...     % Chapter 3 describes...
As shown in \cref{fig:results}...  % As shown in Figure 4.2...
See \cref{tab:a,tab:b,tab:c}...    % See Tables 2.1, 2.2, and 2.3...

Managing Long Documents

Compiling Chapters Individually

For faster compilation during writing:

% At the start of main.tex:
\includeonly{chapters/methods}
 
% Your \include statements:
\include{chapters/introduction}
\include{chapters/literature}
\include{chapters/methods}      % Only this compiles
\include{chapters/results}
\include{chapters/conclusion}

Comment out \includeonly for the full document.

Draft Mode

Speed up compilation during writing:

\documentclass[12pt, draft]{report}

Draft mode:

Shows overfull/underfull box warnings
Replaces images with placeholders
Compiles faster

Compile Workflow

For the final document:

pdflatex main
bibtex main
pdflatex main
pdflatex main

Yes, run LaTeX three times for all references to resolve.

Thesis-Specific Tips

Consistent Terminology

Define terms once:

% In preamble
\newcommand{\myterm}{Specific Technical Term}
\newcommand{\mytool}{\textsc{ToolName}}
 
% In text
We used \mytool{} to analyze \myterm{} data.

TODO Notes

Track what needs work:

\usepackage[colorinlistoftodos]{todonotes}
 
\todo{Need to add more citations here}
\todo[inline]{Rewrite this section}
\missingfigure{Chart showing results}
 
% Get a list of all todos:
\listoftodos

Revision Tracking

For advisor feedback:

\usepackage{changes}
 
\added{New text added}
\deleted{Text removed}
\replaced{new text}{old text}
 
% Or simpler highlighting:
\usepackage{soul}
\hl{Highlighted text for review}

Common Thesis Problems

Overfull Boxes

Overfull \hbox (12.3pt too wide)

The text extends past the margin. Solutions:

Let LaTeX break the word: \hyphenation{prob-lem-at-ic}
Force line break: \\
Allow slight margin overflow: \sloppy (last resort)

Figure Placement

Figures floating to wrong locations:

% Force figure here
\begin{figure}[H]  % Requires float package
 
% Or adjust float parameters
\renewcommand{\topfraction}{0.9}
\renewcommand{\bottomfraction}{0.9}
\renewcommand{\textfraction}{0.1}

Bibliography Not Appearing

Ensure you cite at least one source
Run BibTeX after LaTeX
Check .bib file is in the right location
Verify \bibliography{} points to correct file (without .bib extension)

Pre-Submission Checklist

Before submitting:

[ ] All chapters compile without errors
[ ] All references resolve (no ??)
[ ] All citations exist (no missing references)
[ ] Page numbers are correct
[ ] Table of contents is up to date
[ ] List of figures/tables is complete
[ ] Bibliography is complete and formatted correctly
[ ] Margins meet requirements
[ ] Line spacing meets requirements
[ ] Figure quality is sufficient for printing
[ ] PDF is searchable (not scanned images)

Backup Strategy

A thesis represents years of work. Protect it:

Version control: Use Git for all files
Cloud backup: Sync to cloud storage
Multiple locations: Keep copies in different places
Regular commits: Commit after each writing session

git init
git add .
git commit -m "Initial thesis structure"
# ... work ...
git commit -m "Completed methods chapter first draft"

Conclusion

Writing a thesis in LaTeX takes effort to learn, but pays dividends:

Consistent formatting throughout
Reliable cross-references
Professional typography
Easy bibliography management
Handles 100+ pages without problems

Start with your university's template, organize your files well, and build your document incrementally. By the time you're done, you'll have a professional document you're proud to submit.

The thesis itself is hard enough. Let LaTeX handle the formatting so you can focus on the research.

The 3 AM Formatting Nightmare

Before You Start

Get the Right Template

Organize Your Files

Document Structure

The Master Document

Front Matter

Chapters

Essential Packages

The Preamble

Package Recommendations

Figures and Tables

Figure Organization

Subfigures

Tables

Bibliography Management

BibTeX Basics

Citation Commands

Bibliography Style

Cross-References

Labels

Smart References with cleveref

Managing Long Documents

Compiling Chapters Individually

Draft Mode

Compile Workflow

Thesis-Specific Tips

Consistent Terminology

TODO Notes

Revision Tracking

Common Thesis Problems

Overfull Boxes

Figure Placement

Bibliography Not Appearing

Pre-Submission Checklist

Backup Strategy

Conclusion

Frequently Asked Questions

Related Articles

Best LaTeX Thesis Templates for 2025: A Curated Collection

Mastering LaTeX Bibliographies: The Complete Guide to Saving Hours on Citations

LaTeX in 15 Minutes: From Zero to Your First Document

The 3 AM Formatting Nightmare

Before You Start

Get the Right Template

Organize Your Files

Document Structure

The Master Document

Front Matter

Chapters

Essential Packages

The Preamble

Package Recommendations

Figures and Tables

Figure Organization

Subfigures

Tables

Bibliography Management

BibTeX Basics

Citation Commands

Bibliography Style

Cross-References

Labels

Smart References with cleveref

Managing Long Documents

Compiling Chapters Individually

Draft Mode

Compile Workflow

Thesis-Specific Tips

Consistent Terminology

TODO Notes

Revision Tracking

Common Thesis Problems

Overfull Boxes

Figure Placement

Bibliography Not Appearing

Pre-Submission Checklist

Backup Strategy

Conclusion

Frequently Asked Questions