Earlier today, an Apple spokesperson confirmed the existence of an iOS vulnerability related to the way PDF documents are handled. The vulnerability allows the execution of third party code when the end user happens to download a specially crafted PDF file.
According to Apple, engineers are aware of the issue and already developed a fix that will soon be released via a software update. No dates have been given, so until then, you may want to shy away from PDF documents coming from untrusted sources in order to avoid any potential issue with your iPad.
Note that the same vulnerability was used by white hat Comex to make his new jailbreaking method easily available via jailbreakme.com, so if you plan to jailbreak your iPad, be aware that you will no longer be able to use this method after the update.