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I have a 64GB USB stick which I want to use on both my (Mountain Lion) iMac and my (work) Windows 7 laptop. I don't want to or need to share files across platforms and require the following structure:

Partition 1 - Mac OSX Journaled case-sensitive Encrypted Partition 2 - Windows FAT 32 (not encrypted)

Each method I have tried doesn't work as it appears that to allow encryption on the Mac partition, the root partition scheme needs to be GUID. Doing this means my windows machine can't see the (FAT32) windows partition.

If I set the partition scheme to MBR, disk utility doesn't show the option to format the Mac partition as encrypted.

It may be that there's just not a solution to this and I'll need to carry 2 USB sticks or get into sparse disk images, but confirmation of this would be useful. I've read similar posts on the stack exchange & elsewhere but none seem to cover the exact same set-up.

Many thanks for any help

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If you don't actually require case-sensitivity, Truecrypt is a free and open-source encryption system that will allow you to do either encrypt an entire volume using the Mac OS Extended filesystem or make a encrypted file container (basically an encrypted folder) that can be used to save files as if it were a separate volume.

You will need to download the program from the link above and install it. The Truecrypt program itself will allow you to create encrypted volumes/file containers and mount the encrypted volumes or file containers to your system to use them.

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    Furthermore, Truecrypt is a great solution that works cross-platform with Linux support in addition to OS X and Windows. You can have multiple encrypted partitions or even the entire disk encrypted. If you use an MBR partitioned disk with a FAT formatted partition, encrypted by TrueCrypt, both your OS X and Windows computers should be able to use the disk. But you will need TrueCrypt to decrypt it. I think there may be a portable version, though. Which you would be able to run off an unencrypted partition of the USB drive. – superriku11 Nov 22 '13 at 17:37
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You should be able to create a hybrid GPT+MBR partition table to let both OSes see their volumes. Hybrid partition table aren't standard (they try to comply with the important bits of two different -- conflicting -- standards), so there are some potential gotchas. This page from Rod Smith has a good explanation, and covers how to use his gdisk tool to create them. You might also be able to use the (simpler but less flexible) gptsync tool, which simply clones the GPT table into an MBR -- but I'm not sure if it's smart enough to deal with an encrypted partition.

BTW, I'm not clear on why a GPT-only setup isn't working. According to Microsoft, Windows 7 should be able to use a GPT-formatted disk:

Q. Can Windows 7, Windows Vista, and Windows Server 2008 read, write, and boot from GPT disks?

A. Yes, all versions can use GPT partitioned disks for data. Booting is only supported for 64-bit editions on UEFI-based systems.

...so there may be something else going on.

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