open the case and take a look at MB at first
It will only take you 10 minutes to identify if the USB slots have been damaged.
As somebody suggested, what you can try:
1. check device manager ---USB device if there is a yellow mark
2. if yes, reinstall USB driver but normaly it is included in MS ITB already
3. check CMOS settigns
Even it is HW related, it should be able to fix it by jump wire without replacing either SB or MB. Tell us your exact model, I might be able to figure out how much it needs to get thing done.