If your system is running you can check your firmware and update it following this Apple TN: [http://support.apple.com/kb/HT1237|EFI and SMC firmware updates for Intel-based Macs].
If your firmware is damaged you will need to replace the EFI EEPROM chip after you have burn't it with a fresh image.
If you bring your system in to an Apple Store they maybe able to fix it for you under extended warranty. If you bring it into an authorized services system they will only replace the logic board and not under warranty.