USB Ports not working

You didn't mention what model Mac Pro you have, nor which USB ports aren't working. I'm going to guess it's an older model (2008 or so?) 8-core model and its the ports on the front that aren't working. If so, this is a fairly well known problem:

http://forums.macrumors.com/showthread.php?t=231251
http://discussions.info.apple.com/message.jspa?messageID=7354084

I believe there's a procedure for reseating the connectors on the motherboard that run to the front USB ports; if I find it, I'll post more.

DMW

Here's some USB tips.

Apple's USB quick assist.

DALE

I am having the same problem as well. My computer is pre-2008 and neither USB port works unless connected to my iPhone or iPad. Not good. Also looking for a solution.

I had the same problem when connecting my Blackberry Bold to my 08 Mac Pro - all other USB devices would either A) stop working or B) work sporadically. When I disconnected the Blackberry, everything was fine. Apparently the amount of power supplied to the USB system isn't very much (thus the "green" power consumption) and would shut down when I plugged my Blackbery into a port. Try connecting 1 device at a time until you find the culprit.

Recently I opened hard drive on desktop but an external hard drive plugged into either of the two USB ports stopped being recognized on our Macbook Pro. Reset PRAM but still not recognized. Opened Disk Utility and could see the external drive on the left. Clicked on the external drive and selected Verify Disk. After it finished, at the bottom of the screen "Mount Point" listed Volumes/Name of the Drive. Clicked on Volume/Name of Drive and window opened with icon for the external drive. Dragged the icon over to the window below icon Macintosh HD. After doing this, plugged in several different external drives (e.g. My Book or Corsair) and open the hard drive - the external drives show up. Also rebooted multiple times and still works. Hope this helps.