The effect of the exchange-correlation potential in ab initio electron transport calculations is investigated by constructing optimized effective potentials using different energy functionals or the electron density from second-order perturbation theory. The authors calculate electron transmission through two atomic chain systems, one with charge transfer and one without. Dramatic effects are caused by two factors: changes in the energy gap and the self-interaction error. The error in conductance caused by the former is about one order of magnitude while that caused by the latter ranges from several times to two orders of magnitude, depending on the coupling strength and charge transfer. The implications for accurate quantum transport calculations are discussed.