Respiratory complex I plays a central role in energy transduction. It catalyzes the oxidation of NADH and the reduction of quinone, coupled to cation translocation across the membrane, thereby establishing an electrochemical potential. For more than half a century, data on complex I has been gathered, including recently determined crystal structures, yet complex I is the least understood complex of the respiratory chain. The mechanisms of quinone reduction, charge translocation and their coupling are still unknown. The H+ is accepted to be the coupling ion of the system; however, Na+ has also been suggested to perform such a role. In this article, we address the relation of those two ions with complex I and refer ion pump and Na+/H+ antiporter as possible transport mechanisms of the system. We put forward a hypothesis to explain some apparently contradictory data on the nature of the coupling ion, and we revisit the role of H+ and Na+ cycles in the overall bioenergetics of the cell.