The IKS K+ channel plays a major role in repolarizing the cardiac action potential. It consists of an assembly of two structurally distinct α and β subunits called KCNQ1 and KCNE1, respectively. Using two different expression systems, Xenopus oocytes and Chinese hamster ovary cells, we investigated the effects of external protons on homomeric and heteromeric KCNQ1 channels. External acidification (from pH 7.4 to pH 5.5) markedly decreased the homomeric KCNQ1 current amplitude and caused a positive shift (+25 mV) in the voltage dependence of activation. Low external pH (pHo) also slowed down the activation and deactivation kinetics and strongly reduced the KCNQ1 inactivation process. In contrast, external acidification reduced the maximum conductance and the macroscopic inactivation of the KCNQ1 mutant L273F by only a small amount. The heteromeric IKS channel complex was weakly affected by low pHo, with minor effects on IKS current amplitude. However, substantial current inhibition was produced by protons with the N-terminal KCNE1 deletion mutant Δ11-38. Low pHo increased the current amplitude of the pore mutant V319C when co-expressed with KCNE1. The slowing of IKS deactivation produced by low pHo was absent in the KCNE1 mutant Δ39-43, suggesting that the residues lying at the N-terminal boundary of the transmembrane segment are involved in this process. In all, our results suggest that external acidification acts on homomeric and heteromeric KCNQ1 channels via multiple mechanisms to affect gating and maximum conductance. The external pH effects on IKr versus IKS may be important determinants of arrhythmogenicity under conditions of cardiac ischaemia and reperfusion.