A serial interface for a programmable logic device substantially eliminates skew across multiple channels both in the receiver and in the transmitter. Even when the channels are independent (e.g., are in different quads), skew is substantially eliminated by monitoring to determine when all channels have reached their active states (i.e., in the case of receiver channels when all channels have achieved byte alignment and have received an alignment character, and in the case of transmitter channels when all transmit PLLs have locked), and only then allowing data to flow between the serial and parallel domains.