A method of compensating for a byte skew of a PCI Express bus, the method including determining whether received data are in a training sequence or not, setting an alignment point corresponding to each of the lanes based on a comma symbol included in the training sequence when the received data are in the training sequence, and shifting the alignment point by reflecting an addition or a removal of a skip symbol on the received data through each of the four lanes when the received data are not in the training sequence. Therefore, the byte skew of the PCI Express bus may be effectively compensated for despite the addition or the removal of the skip symbol.