5V input COMPATIBLE ALTERA FPGA FAMILY

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Now whether if pin is configured as PCI I/O can I give 5V input (General Input) and will it not affect the performance of device or damage it.

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Read the data sheet or handbook for the device.

Most PCI clamping diodes are there to clamp overshoot, not a DC level.

If you know what device you are going to use, try to find the schematics for a PCI evaluation board that uses the device and see what they did.

Keep in mind that most PCI buses will in fact be 3.3V, so you may need to support both voltages. As I said earlier, this is where bus switches are useful, as it makes it easy to create a universal PCI board.

Cheers,

Dave