How to create links in the Zettelkasten Method: A PhD Student's Guide to Smart Note-Taking

German sociologist Niklas Luhmann published more than seventy-five books and five hundred articles by simply following a certain style of note-taking (known as Zettelkasten — or slip box). When I first learned this, I thought the secret was in writing better individual notes. I was wrong.

When I started my PhD, I spent more time than i care to admit crafting what I believed were perfect notes. I would carefully summarize articles, organize them into neat folders, and feel satisfied with my growing collection. The problem? When it came time to write, I found myself staring at hundreds of isolated notes that seemed to have no relationship to each other. I had information, but I couldn't see how it connected to form arguments or insights.

This frustration led me to discover the real power of the Zettelkasten method. The challenge isn't writing good notes - it's creating meaningful connections between them. A Zettelkasten has been described as a conversation partner, but this only works if you properly "feed" it with interconnected ideas rather than isolated fragments.

The Zettelkasten (meaning "slip box" in German) was developed by Luhmann as a physical system of index cards. While variations of this system date back to the 17th century, I've found it particularly valuable for PhD work because it encourages taking smart notes that are short, concise, and in your own words. The key is always noting why this information matters in a way you'll understand later.

Through my experience (and many failed attempts), I learned that the goal isn't simply to accumulate knowledge. Instead, you want to create a personal wiki that reflects your research interests and provides the context you need for your dissertation and academic writing. This became especially important as I realized that PhD students must synthesize vast amounts of information into coherent arguments - something that isolated notes simply cannot support.

I hope that sharing my approach to creating effective links will help you avoid the same mistakes I made. The method involves three primary connection techniques: folgezettel (alphanumeric IDs), direct links between notes, and strategic tagging. I'll explain how these systems work and show you when and why to use each one to turn your isolated notes into a powerful thinking tool.

Understanding Links in the Zettelkasten Method

Having established why connections matter more than individual notes, let me explain how this system actually works. The Zettelkasten transforms isolated notes into a dynamic network of interconnected ideas, but understanding the mechanics is crucial for making it work effectively.

What is the Zettelkasten method?

The Zettelkasten method is a personal knowledge management system that differs fundamentally from traditional note-taking approaches. The term "Zettelkasten" translates to "slip box" or "note box," referring to the physical or digital space where notes are stored and organized.

At its core, this method involves breaking down complex ideas into smaller, manageable atomic notes, each containing a single idea or piece of information. This is where most people struggle initially - they want to capture everything about a topic in one comprehensive note. Instead, the system employs a bottom-up approach where organization emerges through connections between notes rather than predefined categories.

The difference is significant. Traditional note-taking asks "Where should I file this?" The Zettelkasten asks "How does this connect to what I already know?"

Why linking is central to Zettelkasten

Here's what I discovered during my first year of PhD work: without connections, even the best notes become isolated islands that you'll never find again. The linking mechanism is the engine that drives creativity and knowledge growth. With proper links, your notes form a navigable archipelago where each note can be discovered from multiple entry points.

The process of linking related notes stimulates creative thinking and helps you discover novel connections between seemingly unrelated concepts. I've found this particularly valuable when working on literature reviews - connections often reveal gaps in existing research or highlight contradictions between studies. These connections extend your mind and memory because the structure mimics how your brain works.

When implemented correctly, a properly linked Zettelkasten becomes what Luhmann called a "conversation partner". This isn't just academic jargon - I regularly find myself following unexpected pathways through my notes that lead to insights I couldn't have planned. The knowledge relationships you create significantly improve recall and train your mind to see patterns.

Types of links: direct, folgezettel, and tags

Three primary linking mechanisms create different relationship types in your knowledge network. Each serves a distinct purpose, and understanding when to use each one prevents the system from becoming overwhelming.

1. Direct links are the strongest type of connection, explicitly coupling two notes to each other. These links should include context explaining why the connection exists. For example, instead of simply linking to "cognitive load theory," you might write "contradicts the findings in cognitive load theory regarding working memory limitations." Direct links create a 1:1 relationship that remains manageable even as your system grows.
2. Folgezettel (meaning "subsequent note") creates a hierarchical sequence. This approach assigns each note a unique ID, establishing its position within a chain of thought. Unlike direct links that can connect across topics, folgezettel creates parent-child relationships within a branch. Think of it as creating a trail of breadcrumbs that shows how your thinking developed on a particular topic.
3. Tags or keywords form the weakest but still valuable connection type. They decouple related notes from one another—notes about "#banana" don't need to know about each other, yet they form a cluster. Tags can be thought of as "virtual folders" since they delineate subsets of your entire Zettelkasten. I use tags sparingly, primarily as entry points for broad themes rather than detailed categorization.

Each connection type serves different purposes: direct links for explicit relationships, folgezettel for sequential development, and tags for thematic grouping. The key is using them together rather than relying on just one approach.

How to Create and Use Folgezettel

Folgezettel represents one of the most distinctive aspects of Luhmann's original technique. When I first encountered this concept, I'll admit I was skeptical. The idea of assigning seemingly random alphanumeric codes to notes felt unnecessarily complicated. However, after struggling with my traditional folder-based organization system, I decided to give it a try.

What is a folgezettel?

The term "folgezettel" (literally "subsequent note") goes beyond simple sequence - it establishes a specific parent-child relationship between notes. Unlike random placement, folgezettel creates an intended connection through position, allowing ideas to branch organically. This connection might continue a thought, add a new idea to an existing one, or even mark a deliberate end to a line of thinking.

Think of it this way: when you have a conversation, one idea naturally leads to another. Folgezettel captures this organic flow in your note-taking system. The beauty lies in its flexibility - the position has minimal semantic meaning, freeing you from perfect categorization anxiety. As Luhmann himself noted, "Given this technique, it is less important where we place a new note".

Folgezettel essentially creates a tree-like structure (termed Folgezettel Heterarchy) for your knowledge system. This differs from rigid hierarchical filing systems where everything must fit into predetermined categories. Instead, your notes can branch wherever your thinking takes you.

How to assign IDs and maintain sequence

To implement folgezettel, follow these straightforward steps:

1. Start with primary notes using simple numbers (1, 2, 3...)
2. Branch into sub-notes using letters (1a, 1b, 1c...)
3. Create further branches when needed (1a1, 1a2, 1a3...)

Despite this tree-like structure, notes appear linearized in the archive: 1, 1a, 1b, 2, 3.... The key advantage? There's always space between any two numbers - allowing insertion of related ideas whenever discovered.

For example, if you have notes 1 and 2, you can later insert 1a between them when you discover a related idea. This flexibility eliminates the frustration of trying to force new insights into rigid categories.

Digital systems offer additional options for marking folgezettel relationships. You can place "#" at the end of a link (like "[[target-note]]#") to establish the current note as parent to the linked note.

When to use folgezettel over other links

Folgezettel shines by forcing at least one connection during note creation. Every time you create a new note, you must decide where it fits in your existing structure. This provides a "paper trail" showing how ideas were initially contextualized, giving you a bird's-eye view without opening individual notes.

I've found folgezettel particularly helpful when working through complex theoretical frameworks where hierarchical relationships matter. When I was developing my understanding of cognitive behavioral therapy techniques, folgezettel allowed me to branch from general CBT principles (note 15) to specific techniques (15a, 15b) and then to particular applications (15a1, 15a2).

Although direct links offer more explicit relationships in digital systems, folgezettel remains valuable for PhD students by encouraging deliberate placement and reducing decision fatigue. Instead of agonizing over perfect categorization, you simply ask: "What note does this naturally follow from?"

Remember: folgezettel isn't about rigid categorization but providing structure that facilitates discovery across your academic research.

Using Tags and Direct Links Effectively

While folgezettel connects notes sequentially, tags and direct links create additional dimensions in your knowledge network. I've found that these linking methods can either propel your research forward or create overwhelming clutter - the difference lies in how you use them.

How tags help in thematic grouping

Tags serve as doors into your Zettelkasten, providing thematic entry points to related ideas. Unlike rigid categories, tags create flexible clusters where notes can belong to multiple groups simultaneously. This mirrors how our brains naturally associate concepts across domains.

There are two distinct approaches to tagging: topic tags versus object tags. Topic tags cast wide nets (#diet including everything nutrition-related), whereas object tags target specific concepts (tagging only notes explicitly about the concept of dieting). As your collection grows, object tagging proves more precise and sustainable.

For PhD research, I recommend using tags primarily as search context definers rather than exhaustive grouping mechanisms. This keeps your system navigable even as it expands to hundreds or thousands of notes. The key is restraint - I learned this after creating so many tags that finding anything became nearly impossible.

Creating contextual links between notes

Direct links form the strongest connections in your knowledge system, actively coupling two notes together. The power of these connections comes from their contextual nature - each link should include a brief explanation of why the connection exists.

This "link context" transforms arbitrary connections into meaningful pathways for future exploration. Without context, you'll eventually forget why you connected the ideas. Consider adding phrases like "contradicts the findings in note X" or "provides empirical support for theory in note Y."

Remember that backlinks automatically appear when you link to a note, creating bidirectional relationships. These connections become even more valuable when note titles clearly express content. When I write a note titled "Working memory limitations affect reading comprehension in older adults," I immediately know what that note contains without opening it.

Avoiding over-tagging and link clutter

The biggest pitfall in knowledge management is creating too many connections with little meaning. This creates cognitive overload that makes finding valuable links increasingly difficult.

Avoid broad category-style links like [[school]] or [[work]]. Instead, link to specific ideas: [[working to live depends on meaningful jobs]]. Similarly, prevent tag bloat by questioning whether each tag truly adds value or merely creates noise.

As your system grows, periodically review your tagging practices. Consider creating hub notes or structured indexes for broader topics with many connections. These serve as organized entry points that prevent feeling lost among countless interconnected ideas. I typically do this review every few months - it's like weeding a garden to keep the valuable connections visible.

Organizing Notes with Topic Clusters and MOCs

_{Image Source: Obsidian Forum}

Once my Zettelkasten contained several hundred notes, I faced a new challenge. The individual connections worked well, but I began to feel lost in my own system. I could follow links between notes, but I couldn't see the bigger picture of how my research was developing. This is when I discovered the value of topic clusters and maps of content.

What are topic clusters?

Topic clusters emerged naturally in my system as collections of related notes that formed knowledge neighborhoods. Unlike the rigid categories I used during my master's studies, these clusters developed organically as connections multiplied between related ideas. They function as areas where conceptually related notes reside near each other, creating a dynamic network that grows alongside your understanding.

The beauty of topic clusters is that they don't require upfront planning. Instead, they reveal themselves as you work. For example, as I researched anxiety disorders, I noticed that certain notes about diagnostic criteria, treatment approaches, and theoretical frameworks naturally gravitated toward each other through my linking patterns.

Difference between structure notes and maps of content

Structure notes and maps of content (MOCs) serve similar purposes with important distinctions. Structure notes function like tables of contents, organizing related notes into meaningful sequences or hierarchies. They add structure to sets of notes, providing better overview than simple tags or links alone.

MOCs float at the top level of your Zettelkasten, often organizing multiple structure notes beneath them. As Sascha Fastner describes, "I not only had structure notes that structure content notes, I also had structure notes that mainly structured sets of structure notes."

Think of structure notes as organizing individual chapters, while MOCs organize the entire book. Both serve essential functions, but at different levels of your knowledge system.

When to create a structure note

I recommend creating a structure note whenever you notice specific patterns in your work:

1. Mental squeeze points where you feel overwhelmed by related notes
2. Six or more notes clustering around a central topic
3. A need to visualize relationships between connected ideas
4. Early stages of a writing project requiring organization

The beauty of structure notes lies in their flexibility - they grow organically day by day without following rigid rules. One structure note about photography might evolve very differently from one about Zettelkasten methodology. Don't worry about getting the structure "right" from the beginning. Instead, let it develop as your understanding deepens.

How to build a map of content for complex topics

For complex topics spanning multiple areas, MOCs provide essential navigation tools. During my PhD, I created MOCs for major theoretical frameworks that connected across different research domains.

Start by identifying the highest-level concept that encompasses your research area. Then gather links to relevant structure notes and individual notes that directly relate to this concept. Arrange these links in a meaningful sequence that reflects your understanding of how ideas connect.

The key is to refactor your MOCs as understanding deepens. When sections become too large, break them into sub-structure notes while maintaining links to the parent MOC. This creates a flexible organizational system that adapts to your evolving knowledge landscape.

Remember that MOCs aren't meant to be perfect from the start. They serve as scaffolding that supports your thinking as you develop more sophisticated understanding of your research domain.

Conclusion

Congratulations. You made it to the end, and I hope you have gained an understanding of how to create meaningful connections in your Zettelkasten system. Looking back at my PhD journey, I can honestly say that mastering the art of linking notes has proven far more valuable than simply collecting them. The system truly comes alive when folgezettel, direct links, and tags work together as complementary methods rather than competing approaches.

What surprised me most was how quickly things changed once I started implementing these techniques. Instead of frantically searching through disconnected information, I could follow well-established pathways through my notes. Patterns emerged that significantly shaped my theoretical framework and writing process. The real breakthrough came when I realized that my note collection had transformed from a static archive into what Luhmann called a "conversation partner."

This transformation didn't happen overnight, and I made plenty of mistakes along the way. Sometimes I over-tagged notes, creating more noise than signal. Other times I avoided creating structure notes when I desperately needed them, leaving me overwhelmed by clusters of related ideas. However, each mistake taught me something valuable about how my mind works and how to better support my thinking process.

The system might seem technical at first glance, but the effort invested pays tremendous dividends. Unlike traditional hierarchical organization, Zettelkasten adapts to how your mind actually works - making connections across domains and allowing ideas to develop organically. This became especially important as my research evolved and I needed to synthesize information from multiple fields.

Remember that the ultimate purpose of this system isn't perfect organization but supporting your thinking and writing. The real magic happens when you follow unexpected connections, discover surprising relationships between concepts, and generate insights that wouldn't have emerged from isolated notes. I've found that some of my best ideas came from following link trails that seemed tangential at first but led to important discoveries.

I wish you the best of luck on your academic journey. The approach I've shared will not only help you manage vast amounts of information but also generate the original insights expected in doctoral-level work. Most importantly, you'll develop a powerful thinking tool that grows alongside your understanding - something that will serve you well beyond your PhD.