Methods and apparatus for aligning the transmitters of two or more bidirectional ports of an integrated circuit (IC), particularly an application-specific IC (ASIC) or field-programmable gate array (FPGA). Misalignment of two or more transmitters is determined by the IC itself without the use of external test equipment. Receivers of the bidirectional ports whose transmitters are to be aligned are used by the IC to detect misalignment. Any misalignment of the receivers is also determined and either eliminated or taken into account when aligning the associated transmitters. Variants for ICs with and without internal loop-back capability and for ICs with and without differential outputs are described.