Frequently Asked Questions


Can Highlights extract annotations made with other apps?

Yes, Highlights uses standard embedded annotations which are supported by most PDF readers on both macOS and iOS/iPadOS.

Some PDF apps (including Skim) and most reference managers use non-standard annotations which are not compatible with Highlights. However, most of these apps allow you to export the PDFs with embedded annotations which will work in Highlights.

How do I customize what is included in each annotation?

You can set which information should be included in each annotation (including author, modification date and color category). This is available from the Customize panel in Preferences on macOS and the Format Note icon in the top toolbar on iOS. On compact screens the Format Note menu is available from the More icon.

How do I use citation lookups?

Markup the text of a citation in the PDF using either highlighting, underlining or strikethrough. Tap the annotation and tap the link button. Highlights will attempt to fetch the citation. Citations are sorted at the bottom of your notes. This feature requires Highlights Pro.

How do I use color coding?

Color coding allows for sorting annotations into categories based on their annotation color. You can customize the order and name each category. This is available from the Customize panel in Preferences on macOS and the Format Note icon in the top toolbar on iOS. On compact screens the Format Note menu is available from the More icon.

Power Users

Can I have a standard color for each type of annotation?

Yes, set what color you want for each type of annotation in Settings on iOS/iPadOS or Preferences –> Annotation on macOS. This feature requires Highlights Pro.

Is there tagging support in Highlights?

Yes, Highlights supports per file tagging. Select a color for Tags in Preferences –> PDF –> “Underlining power tools”. Underline the words or short sentences in the PDF you want to use as a tag with the selected color. Tags will be embedded as PDF keywords and exported as Finder-tags when saving.

In addition, Highlights supports per annotation tags “Split files” is enabled in Preferences –> Export. To use this feature as add tags as comments to the annotation using the syntax @tagname e.g. @important or @review. The tags will be added as Finder-tags to the file representing that annotation when exporting as split HTML/Markdown files or to DEVONthink.

Does Highlights integrate with any reference managers?

Yes, Highlights integrates with Bookends (tutorial here) and Papers (tutorial here) on macOS. This feature requires Highlights Pro.

Is Highlights scriptable?

No, not yet.


My extracted annotations show up with redundant text, why?

This happens when the PDF is exported from Skim as it saves a backup of the highlighted text in the comment-field of the annotation.

Highlights crashed on me, what do I do?

Please email me with as much information as you can provide on when/how/why it crashed (crash reports, screenshots and screen recordings are very helpful).


What version of macOS does Highlights require?

macOS Catalina (10.15)

Why does it not support older versions?

Highlights requires macOS Catalina (10.15) and above for text and table recognition features which uses new machine learning APIs that are not available on older releases of macOS.

Can I open documents as a new tab by default?

Yes, this is a system level setting in macOS: Open System Preferences go to Dock and change the “Prefer tabs when opening documents” option to “Always”. (The default is “In Full Screen Only”).

Open documents in new tab

How do I make Highlights my default PDF reader?

By default macOS uses Preview for opening PDF files, but this can be easily changed to Highlights from the Finder:

Select a PDF file in the Finder open the Get Info panel by right clicking on it and selecting Get Info or using the keyboard (Command + I). In the Get Info panel find the “Open with section” and select Highlights from the drop down menu. Click the “Change all…” button below. A system dialog appears, confirm the change by clicking “Continue”.

Set Highlights as default PDF reader

Why does Highlights restore my windows when I re-open the app?

This is a system level setting in macOS that is on by default, to prevent it open System Preferences go to General and enable the “Close windows when quitting an app” setting.

Open documents in new tab