Someone else may have already answered this question but I just figured out how to highlight PDFs in EV for Windows, at least on a PC that Adobe Acrobat installed (as my laptop does). It's actually pretty simple though surprisingly, it appears to be undocumented. When you select a pdf file in EV, you should see the PDF viewing toolbar appear at the top of the Note/Note Panel. Click on the left-hand most icon, the one that looks like an eye. (When hovering my mouse over it, mine reads "Evernote PDF Reader Powered by Foxit Corporation." That should open the PDF in separate window. (In my case, it opens it in Adobe Acrobat Standard DC. Not sure if you don't have that installed if the file will open in Foxit's Evernote PDF Reader.) With the file open, you can now select the text you wish to highlight and then click on the Highlight icon in the icon bar under the main menu (again, I'm relating what I see in my Acrobat Standard DC configuration... the Evernote PDF Reader may be different). Your selected text should now be highlighted in the default highlight color. Save and close the file. It will be returned to your EV for Windows database, where it the resaved version will now show the highlights you made. I hope that makes sense and works for others, not just me. What was throwing me off was double-clicking on the PDF file and opening it, apparently outside of/disconnected from Evernote, using the highlighting tools and saving the file but then not seeing the file basically disappear (i.e., not redisplay in EV).