Only if you convert them to one of the video formats InDesign supports. I believe those are Flash (F4V, FLV), Quicktime (MOV) or H.264 MPEG4 (M4V). You can use Adobe Media Encoder (included with the Creative Suite) to reencode the files.
Thanks for the answer, but putting a youtube video in a interactive pdf is that possible?
Its only possible if the user is connected with the internet. But how?
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YouTube does provide a Flash API that lets you connect directly to YouTube and stream video from their servers. If you have any Flash/Actionscript skills it would be possible to build a YouTube Flash player, place that in ID and export to an interactive PDF. I've done a bit of PDF testing and the viewer is forced to click through a bunch of security/allow buttons before the clip will play.
Here's an interactive PDF with a Flash player I built awhile back embedded
This won't work inside of a browser, but if you download the pdf and open it in Reader 9 it should work. You'll have to click the Flash icon and Allow dialogs first then enter a YouTube URL in the field in the lower right corner and click play. Most YouTube URLs from your browser address field should work, i.e. this format: