One embodiment describes a fault tolerant transmission system that includes a programmable logic device. The programmable logic device includes a first serial port communicatively coupled to a first serial link, in which the first serial port receives a first transmission signal from the first serial link, and a second serial port communicatively coupled to a second serial link, in which the second serial port receives a second transmission signal from the second serial link. The first serial link and the second serial link are disposed in parallel with each other and communicate over a first single conduit, and the first communication signal and the second communication signal are representative of identical information. The programmable logic device further includes circuitry that detects a fault in the first serial link, the second serial link, or both by comparing the first communication signal and the second, and if a fault is detected, determines whether the transmission system can continue operation despite the fault.