The diuretic drug amiloride is a specific inhibitor of sodium transporting proteins in several cell types. Attempts to inhibit this activity in membrane vesicles derived from various bacteria, did not yield clear results. Therefore, we tested the effect of amiloride and its derivatives on the purified Na+/H+ antiporters of E. coli reconstituted in functional form in proteoliposomes. Whereas NhaA is not inhibited by amiloride, both amiloride and harmaline are potent inhibitors of NhaB with K0.5 of 6 and 15 microM, respectively. The pattern of inhibition by amiloride derivatives is different from that reported for mammalian antiporters but similar to that reported for the Na+/H+ antiporter of D. salina [Katz, A., Kleyman, T.R. and Pick, U. (1994) Biochemistry 33, 2389-2393]. Clonidine is a poor inhibitor (K0.5 = 200 microM) while cimetidine had no effect on the antiporter up to concentration of 1 mM. These new potent inhibitors provide us with important tools for the study of the mechanism of action of NhaB.