The ultimate guide on how to annotate PDF files on the iPad

Ultimate guide on how to annotate PDF files on the iPadFor most people in university and college, the ability to annotate PDF files is one of the main reasons for buying an iPad. There are hundreds of apps out there that let you annotate PDFs: how do you know which one is the best one for you?

Rather than discussing one particular app in detail, this post presents the bigger picture by discussing three different user profiles whose needs are different with regards to PDF annotation and management. Once you know what type of user you are, you can check out the overview of 10 (plus 3) apps, my personal favorites, and some thoughts on using a stylus. With all this information, finding out what app you need to annotate PDF files “your style” becomes a piece of cake.

What type of reader are you?

Because everybody’s reading habits and PDF management requirements are unique, there is no such thing as “the best app to annotate PDF files on the iPad”. What works for you can be a nightmare for your colleague. However, one can make out three different user profiles with roughly similar needs: the Penny Pincher, the All-Around Reader, and the PDF Management Master.

You might fall in between two of these profiles. In this case, you can either decide what requirement is more important for your individual workflow, or you can use two apps for different workflows and different tasks. For example, I am currently using Sente to annotate journal articles and iAnnotate to annotate PDF files for committee work.


The Penny Pincher: Annotate PDF files for free

The Penny Pincher does not want to spend money to annotate PDF filesIf you don’t deal with PDFs very often, there is no big reason to spend money on PDF apps. iOS lets you read PDFs without any additional software needed; however, if you want to annotate PDF files you need an extra app. Luckily, Adobe Reader  and pdf-notes (iTunes links) are two free PDF annotation apps that are powerful enough to let you highlight PDFs and even add sticky notes. pdf-notes is particularly interesting because it lets you change annotation tools through gesture-based shortcuts. The only downturn is that the free version of pdf-notes displays advertisements, which you can get rid of by buying the paid version. Adobe Reader does not display ads.

In general these apps come pretty close to the apps listed in the second category, so you might want to check out these free options before you are investing money on paid All-Around Reader apps. However, these free apps do not substitute full-blown PDF management system apps that are described in the third category.


The All-Around Reader: Using the iPad as the main reading device

Annotate PDF files on your iPadThe serious reader uses the iPad frequently to annotate PDF files, and it might be even his or her main device for reading PDFs. If your PDF reading workflow has one of the two following requirements, your annotating needs are best served by apps for the all-around reader.

If you value flexibility, then the apps in this category are a good fit for you, because you will be able to view annotations you made on the iPad in every other standard PDF viewer on the Mac (e.g., Preview) or the PC (e.g., Adobe Reader).

Another reason why you need an app for the All-Around Reader is that you want to or need to make annotations in a free-drawing mode. For example, many of your PDFs could be just scanned-in images that don’t allow you to select lines of text as you would in a text-based PDF. Another reason might be that you want to make handwritten annotations in the margins of the PDF; however, I am not convinced that this is a good way to annotate PDFs (see below).

If you are serious about annotating PDFs and need to sync your files with a PC, your best bet is All-Around annotation app or Papers from mekentosj.

If one or more of these examples are must-haves for you, then you would fare well with apps like GoodReader for iPad ($5), PDF Reader Pro ($6), PDF Reader Pro Edition for iPad ($10; same name, different company), PDF Expert ($10), iAnnotate PDF ($10), or PDFpen for iPad ($10; iTunes links).

If, however, it is important for you to have your PDF not just lying around in folders but organized in a library, you probably will be more happy with an app targeted for the third user profile.


The PDF Management Master: Integrate the iPad in your read-write-cite workflow

This user profile is for the geeks. While the apps mentioned for the first and second user profile started out as apps to read and annotate PDF files, the apps in this category started out as reference management apps on the Mac and later added companion apps for the iPad that let you annotate PDF files.

This user profile is the best fit for you when you want to have a tightly integrated ecosystem that allows you to find, manage, read, annotate, and cite your PDFs in your academic workflow.

Typically, you would also own the Mac (or Windows) companion app that serves as your main tool to curate your library, to insert in-text citations in your write-ups, and to create bibliographies at the end of your paper. While the iPad apps in this category also allow you to add and manage papers, they lack the powerful citation functions of their respective Mac versions. However, they are great tools to access your library on the go, and it is much more convenient to read and annotate PDF files on the couch with your iPad than at the desk with your Mac.

The biggest benefit of this tight integration is that you can view and edit your highlights and notes regardless of whether you are working with you iPad or with your Mac. Also, storing your PDFs in a library (vs. a simple folder structure) lets you better organize your papers. You can assign one PDF file to multiple collections and you can add keywords, tags, status, and rankings to your PDFs.

In my opinion, if you annotate PDF files as part of your research workflow (maybe you even have some annotation strategies), then PDF management apps are a very good investment for you.

One of the best ways for academics to annotate PDF files is through dedicated PDF management systems.

If you are dealing with a lot of PDFs (and chances are good you do if you are in academia), then you should consider to invest some time and money into a PDF Management System.

However, the power of PDF management systems comes at a price: First, you will not easily see your annotations with apps that are outside your ecosystem (e.g., Preview, Adobe Reader). This is a lesser concern for you, since you sit comfortably in your ecosystem, but it might be a hurdle when you are working with a co-author who does not use a PDF management system.

Second, none of the apps that target this user profile allow you to annotate PDF files in a free-drawing mode. This is not a big concern either, as I find that handwritten annotations are overrated anyways (see below, you are almost there).

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Right now, the only two apps that let you annotate PDF files are Papers ($15) and Sente ($20; iTunes links). You can read a detailed comparison between Papers and Sente here, or even more detailed reviews of each individual app (both iPad and Mac versions) over there: Sente for iPad, Papers Touch for iPadSente for Mac, and Papers for Mac. The reviews for the iPad apps even have videos, so you can experience them (almost) first-hand without spending 15 or 20 bucks up front!

Also, there are three more apps that are targeted to this user profile, but that don’t have the ability to add annotations (yet): Sente Viewer (free), Mendeley (free), and Bookends on Tap ($10; iTunes links). The first two are simply viewers, but Mendely says that Mendely Pro (most likely with annotation support) is in the works. I also expect that Bookends on Tap will add annotation support some time in the future.


A few thoughts on writing margin notes with a stylus

Personally, I believed that the iPad would allow me to annotate PDF files exactly the same way as I was used to do it on paper copies: by squeezing handwritten notes into the margins.But upon reflection, this is actually not the best idea.

The problem with handwritten notes is that they are neither searchable nor easily editable. I therefore prefer nowadays to use sticky notes, and more advanced PDF management system apps such as Sente can display your notes in a separate space, which makes reviewing your papers really fast.

A stylus is useful for some applications on the iPad, but I don’t think that scribbling text into the margins of a PDF is one of them.

Of course, if you are a fan of expressing your thoughts not in pure text but through sketching out diagrams and images, an application that allows you to add free drawings is your best bet.

Read next: What stylus is optimized for handwriting and conceptualizing ideas?


Overview: 10 + 3 apps to annotate PDF files

Once you have identified what kind of user profile matches most closely your own requirements, you can check out what app might be the best fit for you. The table below gives you a first overview (Note: the * indicates that I was able to personally try out the application), but you can also check the button of this page for links to more detailed reviews on the web. (edit: iAnnotate also has a tagging function. Thanks Jojoba for pointing this out! I updated this post with Adobe Reader which is not shown in the table.)

Overview of 13 apps to annotate PDF files on the iPad

This table gives you an overview over the features of the best annotation apps that you can find for the iPad. Sorted by user profile.


What are my favorites?

I am a big fan of PDF management systems because of the ability to sync my entire library across different devices, the powerful organizing system (especially tags and smart folders), and the ability to handle in-text citations and bibliographies.

Another benefit of having a dedicated ecosystem for your PDF workflow has to do with cloud space. Since starting my PhD, my main library has already grown to 1.5 GB of disk space. While dropbox is awesome in helping you to stay in sync, the free account is only 4 GB. If I had all my papers in a dropbox folder, I would quickly run out of my free dropbox space!

Organize, read, and annotate PDF filesOrganize, read, and annotate PDF files

Right now I would say that Papers and Sente (iTunes links) are the leading PDF management systems (see my comparison article here). While they both let you annotate PDF files, their individual offerings are actually quite different from each other, so check out the in-depth reviews on academiPad (links are at the end of this post). UPDATE: Mekentosj has announced its Papers for Windows app.

In terms of more flexible, dedicated PDF readers, I use iAnnotate (iTunes link) to work with non-research related papers (e.g., committee work), and the main reason for this is that iAnnotate was one of the first apps that allowed me to annotate PDF files. I must say though that through writing this post I became interested in trying out two other PDF annotation apps that seem very promising:

The first one is PDFpen for iPad (iTunes link), which is a highly acclaimed newcomer to the field (it won the Macworld 2012 Best of Show Award and the Mac Observer Editors’ Choice 2012 Award). What I particularly like is that PDFpen offers an ecosystem by having established Mac applications next to the iPad app, while at the same time it offers the flexibility to freely draw annotations. Sounds like a winner to me!

PDFpen is the new kid in the gang of annotating apps on the iPad, but the developer Smile on my Mac has plenty of experience in PDF management and annotation on the Mac.

Another app that I was quite positively surprised about is pdf-notes (iTunes link). My first impression was very negative: the free app displays advertisements in its lower left corner, greeted me with bug warnings, and took a long time to load a PDF for the first time (it is much faster after that). But don’t let this discourage you: pdf-notes is clearly on to something with its focus on gesture-based interactions. In iAnnotate, for example, you need to tab a button to switch from annotating to navigating. pdf-notes, on the other hand, lets you annotate PDF files with one finger, navigate with two fingers, and switch your tool with three fingers. Given that the paid version ($10) is ad-free, you should include this one in the list of annotation apps for the serious reader.

Shameless plug: If you found this article useful, I would like to ask you for two things. First, please share this article with others in your social network. The sharing buttons at the left side make this super easy, and you can find more ideas on how to spread the word here. Second, if you want to use your iPad not only for reading but also for serious (academic) writing, please check out my other guide on how to pick a keyboard case that perfectly fits your writing style. Thanks, and enjoy reading and writing!


Appendix: academiPad reviews

Appendix: Other reviews

What app are you using to annotate PDF files? Please let us know in the comment section, and if you like, maybe you can share some thoughts on what makes the app you are using a great app?

Disclaimer: Panorama image, Yoda with iPad image, and overview table by academiPad. This article contains affiliate links.

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  1. Karim says:

    Hi Jo,
    I work for a company that develops a PDF app called Xodo and I have to say that your research and segmentation for the PDF users is simply perfect. You can’t imagine how much this has helped us. Keep it up!

  2. Thanks for the article!
    I use Easy Annotate to annotate my study/research projects.
    What I like most is that it allows me to compare and view two PDFs at the same time. Great feature, as I can now open my study and reference material side-by-side.

  3. George R says:


    I must say I don’t fully agree with the author about handwritten annotations. Yes, they don’t show up in searchable form in the list of annotations. However, together with text notes they present extra information at a glance when you are skimming through the PDF you once read. I personally find it extremely useful, though it very much depends on one’s workflow and diligence in making self-contained notes for each paper they read.

    The inability to add handwritten and textual notes as well as shapes has been one of the things preventing me from switching from GoodReader to Papers. The other thing being that I really appreciate Android OS and did not want to commit to an iOS only app.

  4. thintieguy says:

    I appreciate this article. So far, I have not found exactly what I am seeking. I want to find the fastest, most intuitive way to annotate a PDF with straight lines in a graph format that looks a bit like economic charts. The purpose is to show above a written text the shape of a melody for those who cannot read music. My problem is that the best solution I have found is using my iMac and painstakingly make this kind of graph with Wondershare PDF Editor. Stuck using a mouse, I get cramps in my right hand very quickly and would much rather have a system where I could do this using an iPad and a finger/stylus (I’ve not yet purchased one but would do so if only to accomplish this single task). Also, Wondershare only lets me use straight lines in one thickness and in red (a BIG hassle). Any thoughts out there?

  5. Rohit says:

    Hi Jo,
    Thank you for a very informative article.
    May I request you to please help me with the following queries:
    1) I believe you are using multiple apps – iAnnotate, Sente etc. Are the pdfs portable between these apps. If they are, do the annotations, highlights, etc. also remain intact when the pdf is opened in a different app.
    2) You also touched upon the limited storage capacity on iPad. So, if I remove my older pdfs from ipad to accomodate the new pdfs, what happens to the annotations, highlights on the older pdfs….where are these stored and can these we used again seamlessly.

    – Rohit

  6. Ehud says:

    Thanks for the professional review.
    I downloaded PDFpen. The first look is impressive but then, after about an hour of work, it saved the file. The process took few sec and at the end I saw a brief msg “save failed, aall changes are lost” and indeed they were lost forevever. I tried two more times and for the same outcome (stupid me, I could have predicted that).
    I wrote the PDFpen guys and hope they can find a way around this bug. But as it is now, PDFpen is absolutely useless for me.


  7. Herfried Hartl says:

    Halli Hallo, bin auf der suche nach einen App für mein IPad II zur
    Notenverwaltung – ca. 500 Titel
    (auch3-4seitig) wichtig ist mir eine flotte Suchfunktion für live Auftritte.

    Vielen DANK im VORAUS.


  8. Theo says:

    Hi Jo,

    First thank you for all these very clear and helpfull informations for a Mc dummy like me. I bought yesterday my first Mc device (Ipad4).

    However there one info i find nowhere. I am looking for an app which is doing the following special tricks with pdf files:
    1) With an Original pdf file: annotate (underline, highlight, posts, etc…easy), edit annotation list (classify per type of annotation, for each annotation indicates page number, possibility to select and modify annotations,etc…) and export annotations (in pdf file for example). One example can be: with a study book, i annotate all the formulas and sentences i am interested in to learn, i export it in a file and magic i have my learning document ready and can print it, and may be bring it to the exam…;-)
    2) The same than above but with a pdf file done by scannning a book. This i think more tricky.

    Did you heard about some apps that can do this? I watched the videos of apps you advice for but these tricks are not shown.

    Thank you for your help, and one more time congratulations for your blog!

    Theo from Paris

    • Jo says:

      Hi Theo,
      That is quite specific. The closest thing that comes to my mind is Sente. It won’t export your annotations into a special file or book, but it lists them up front on the cover of the file.
      There might be a better solution, but I don’t know it.
      That won’t work with a scanned book, though.

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