How I Highlight and Take Notes When I Read

I read almost entirely digitally; most narrative non-fiction as Kindle books and most code/software books as PDF. Over time, I am developing a system to help me retain and get more from what I read.


I highlight passages as a way to easily refer back to them. Either in the future or as a part of my Written Narration (see below).

Types of Highlights

There are four main kinds of content that I highlight.

  1. What I don’t understand
  2. What I disagree with
  3. What is a key concept in the material
  4. What really struck me and/or is worth sharing

Not Understanding

If I encounter a new concept or reference I am not familiar with I highlight the text. Maybe it’s a historical reference. Maybe it’s a word I don’t know. Maybe it’s a phrase in another language. These all get flagged so I can look them up or do some research to better understand what I’m reading.


Sometimes I’ll run across a thought or idea that I simply don’t agree with. It may be based on assumptions that I think are faulty. It may be a conclusion that I don’t feel is justified. It may even be something historical that “everyone knew was true” but that later research has proven false.

These can be good points for discussion, especially if I’m reading a book as part of a group.

Key Concept

This is the traditional concept of highlighting; some piece of information that encapsulates a core idea of the chapter or section.

Striking or Sharable

Sometimes there is a bit of text that really strikes you or would be great to share with others. Sometimes this content is a Key Concept, but not always. The litmus test for if something is Striking or Sharable is if the idea that it expresses is self-contained. Can you refer back to this snippet in the future or give it to someone else and have them get the idea without knowing the other concepts which surround it.

Usually this text is shorter (especially if you plan to share it), but not always.

Content Format

Different content formats/platforms have different options for highlighting. My own reading is primarily in Kindle followed by PDF. I am also trying to get better at my Instapaper queue.


I mostly read non-fiction in the Kindle app on my iPad. The iOS Kindle app provides 4 different highlights colors and I use each of these colors for a different highlight type:

  • Not Understanding: Blue
  • Disagreement: Red (named Pink in the app)
  • Key Concept: Yellow (standard color)
  • Striking or Sharable: Orange

This lets me easily scan a book or even filter for a particular color (and therefor meaning) of highlight color.

When I am reading on my Kindle Voyage, I only have access to the Yellow highlight color. This is why I picked Yellow for the Key Concept color. I usually just read fiction on my Voyage and I rarely highlight in fiction. However when I am reading non-fiction, the Key Concept highlight is what I am most interested in.


I tend to read technical books in PDF. These are books that have code samples which don’t display well in Kindle. Again, I am largely reading these on my iPad and my preferred app is PDF Expert. PDF Expert has sufficient annotation tools for me and since it uses iCloud for data storage I have access to my annotated PDFs easily on my phone and on macOS. Additionally, the annotation tools I use are standard PDF tools so I can view an annotated PDF in Preview or other PDF applications.

I don’t annotate in PDFs by color (mostly). Since PDF Expert makes standard annotation tools easily available I tend to use those:

  • Not Understanding: Underline
  • Disagreement: Strike Through
  • Key Concept: Highlight Yellow
  • Striking or Sharable: Highlight Orange (I only discovered that I could change the highlight color while writing this article)

Another great feature of PDF Expert is the ability to see all of my annotations in a single list and easily jump to them. The app lacks the ability to filter my annotations by type, but I haven’t found that to be an issue.


I have developed a large backlog of articles to read in Instapaper but I am starting to work through it due to recent changes in how I manage my time (more on that in a future post). The highlight options in Instapaper are very limited but I wanted to mention it here for completeness.

I just use the standard Highlight feature to designate Key Concepts but I have also setup an IFTTT recipe based on The Sweet Setup article to Save Instapaper Highlights to Ulysses.

Taking Notes

In addition to highlighting, I take notes when I’m reading books (not so much when reading articles, but I have ideas in that direction).

Written Narration

The primary form of note taking is a Written Narration. This is a concept taken from the Charlotte Mason Philosophy of Education which we follow in homeschooling our kids. When I finish a section or chapter, I take a few minutes to write up a basic summary of the material. I will frequently include key or striking quotes as well as my own thoughts or responses to the material.

The goal of the written narration is two-fold

  1. To give myself something tangible that I can re-read in the future to refresh myself on the key concepts of the book
  2. To cement the concepts and ideas of the book in my mind

In support of this second goal, it is important that the written narration be comprised largely of my own words. I endeavor to internalize what I have read and describe it in language and terminology that comes from inside me – to ingest the thoughts and frame them in a way that I really understand them and the ideas become a part of my own treasure-trove of knowledge, ready to be called on in the future.

I keep my written narrations in Ulysses and I will expand on the format in a future post.


In addition to the written narration, I am trying to keep a commonplace book where I write quotes that strike me as worth saving for future reflection or reference. This goes well with my Striking or Sharable highlight category. I capture these into DayOne (in a separate Quotes journal) rather than Ulysses. This is largely so that I can reflect on the quotes when I review past journal entries. It is an interesting reminder of what I was reading at a particular time.

In Closing

My processes are evolving because life is a constant activity of self-improvement. The highlight process has grown out of participation in an online reading group over the last year and the written narration has grown out of seeing our children’s growth and is a habit I’ve been forming over the last couple months. I am seeing benefit in both my retention and general thought processes and am hoping that the benefit will simply continue to increase.