Q: How do I sync my  PDFs from iBooks on my iPad to iBook on my Mini and Maverick desktop?

Have you tried downloading "Calibre" - I use this programme to convert my pdf files to epub, a quick and easy process

http://calibre-ebook.com/download_osx

Click OK and it will convert then just add file to ios X iBooks and sync as usual

My situation got worse,  I think the reason my PDFs would not upload from iBooks on ipad to iBooks in imac even though I told it to fetch them was that I had manual sync selected on the ipad.  I find that ipad memory is easier to manage if I manually manage playlists from iTunes dragging them to I the ipad when I first configure.  This is how it was set up.  However trying to sort out the upload of my PDF library's from ipad to imac I had to sync books.  This then deleted my manual sync settings and re synced my entire ipad ,  at the same time it deleted all the PDFs I had in iBooks on ipad.  Of course it left the collection folders just deleted all the PDFs - the useful part.  So now I have no PDFs in collections but each time I add a PDF to ipad it will sync upto imac when connected to iTunes ,  when I then connect my iphone to imac it will downsync,  this is what I could do with my psion organiser.  This isn't what I need I need automatic sync of iBooks libraries and PDFs by iCloud. Ironic that iBooks syncs purchases via iTunes Store ,  so it looks like iBooks is a commercial ap for storing purchases and PDFs are an afterthought.  Hope this gets fixed or incorporated

Not a brilliant solution but if you delete iBooks on your ipad then download it again from the app store all your collections and PDFs appear as they do on iMac ibooks after syncing with the computer

Thank you for restating your answer, this is EXACTLY what I needed to do!

My problem was similar:  I had books and pdfs on my iPhone that did not appear on iBooks on my MacBook Air.  I followed these instructions:

http://support.apple.com/kb/HT1848?viewlocale=en_US&locale=en_US

A pain in Apple terms as one would hope that they would sync automatically as I have come to expect from Apple, but at least it works.  The company seems to put most of its resources into music in the cloud and has left us readers and writers floundering somewhat [Pages in iCloud is still in beta and is slowly improving, but with many, many bumps along the say]

You have to watch accounts though - I have two as I am one of those benighted individuals who used MobileMe - and when that came in I was forced to create a separate account for MobileMe instead of using my original iTunes account.  Most of my books were purchased or free downloads using my MobileMe account, but you have to make sure you use the same account on each device.

I moved from Android to iOS, Since week I am trying to sync PDF from icloud drive with no luck.  by this post i figure out that icant sync PDF with i cloud.

For now I am using Gooole drive for PDF. 

Hope in future I can sync and read PDF book in iBooks.

To sync books you purchased in the iBook Store go here:

Sync iBooks between devices - Apple Support

To sync pdfs or books you downloaded elsewhere:

iBooks: Viewing, syncing, saving, and printing PDFs on iPhone, iPad, and iPod touch - Apple Support

It seems to me also that if you do it the old fashioned way - that is, connect your IOS device to your Mac with a cable, then you can sync while seeing on the screen what is in each device and moving them that way... sorry I can't be more explicit as I haven't done it for a while and when I do, I just fiddle around until it works.

Ted Smith

Having similar problem, I've been using iBooks for quite a while now, scanning important (to me on the road) docs and storing on my iPhone (driver's license, insurance cards, etc)... works fine syncing between iPhone and MB Pro.  As my library has grown, I decided to spend some time creating "Collections" on my MB, easy task.  However, when I sync, all of my PDFs remain in the "PDF" Collection on the iPhone, iPhone does not receive the "Collections" created on the MB.  I even tried creating the exact same "Collections" on the iPhone but all of the PDFs still sync to the "PDF" collection.  Both iPhone & MB have the preferences set to "Sync Collections".  I ONLY use iTunes, so iCloud is out of the question (I'll never trust any of my personal data on the Cloud).... any advice?

I have the same issue. I had synching between my iphone and ipad (collections, pdfs) etc. Then I upgraded my Mac from Snow Leopard to Mavericks.

Once, I figured out some permission issues* iBooks had ALL of my collections, PDFs) Everything was synching! Then, I did WHAT I believe ruined it.

I deleted my old user account *(originally, I had to create a new account, when upgrading on the Mac to get my icloud to work. I kept the old account in case I needed some documents etc. The old account was my first and last name. The new account I made was first, middle initial, last name. Eventually I deleted the old Mac user account because my iTunes library would not let my Sonos application create a library due to old permissions.

After I deleted the old account, I opened ibooks and noticed that all my PDFs were missing: GONE! The weird thing, all the collections (sub categories of pdfs) I had made on my ipad/phone were still there, just not the content.

I have signed out of iClould on the Mac, signed back in, still does not appear as it did when I first upgraded. Very frustrating.

Mac - 10.9.5

iphone 6 - iOS 8

ipad 4 - iOS 8

From apple.com support site at

iTunes: Transferring media from your iPhone, iPad, iPod touch, or iPod - Apple Supporthttp://support.apple.com/en-us/HT1209

Wah wah.

I have an iPad with lots of .pdf files I downloaded into iBooks. Recently purchased a MacBook Pro & wanted to have the same .pdf files on it's iBook too.

Read lots of posts saying it can't be done. Thought to myself I'd give it a try, so I cable connected the iPad to the Mac. I signed into iTune store, went to "File",

"Devices", Transfer  purchases (even though the .pdf files were not purchased) from iPad. I noticed there was file transferring happening so I waited until it was finished. Then I went into iBook on the Mac & saw lots of .pdf files showing on the list, but each file under List showed "Zero KB" & thought to myself that it didn't work. For giggles, I double clicked on a file & it opened a several hundred page .pdf file!   While it appeared to me that the file transfer messed up my .pdf file names, who cares? At least it worked & the file names can be renamed again.

AIRDROP THE FILES FROM YOUR MAC TO YOUR IPAD - THEN OPEN IN IBOOKS!!

>> spotlight - ibooks - open that folder - select all pdf's you want to transfer - share - airdrop - BOOM!!

Had this problem myself and came to this miraculous realization while beating my head against my iPad!

SSensational help. but why is it so last century? This is Apple - sync usually requires no such effort.  Thank you for helping me avoid a meltdown.

Thank you SOOOOO much. I'd been researching everywhere trying to figure out how to do this. I couldn't find any clear, concise directions until I found this post. It worked like a charm!

Thank you. This worked - when a long and fruitless phone call with Apple support in which I ended up deauthorizing all devices, changing Apple ID and passwords did not. But, how ridiculous is it that iBooksdoes not sync. Before Apple add anything out of this world to what will obviously be iPhone 7 could they please fix some basics like this. And no I don't want to use my Kindle or a third party app to achieve the same result. I like the iBooks interface so what I want is iBooks to work in a seamless and logical way. Of course it's rare in this life that gets what one wants when one wants but maybe one day when I too am in the Cloud...