Lon protease, an ATP-dependent protease in Escherichia coli, degrades abnormal proteins and regulates several important cellular functions. Here we show novel inhibitory effects of lipopolysaccharide (LPS) on Lon protease activities. LPS inhibited the peptidase, protease, and ATPase activities of Lon; and a dose-response study showed that LPS at low doses more effectively inhibited the ATPase activity than the peptidase one, suggesting different susceptibility to LPS of these activities associated with Lon. Structure-activity relationship studies revealed that ReLPS, detoxified LPS, and mono-phosphoryl as well as diphosphoryl lipid A, also showed similar inhibition, suggesting that neither O-antigen polysaccharide nor O-acyl chain, but rather phosphate groups in the lipid A domain, seem to have been responsible for the inhibitory effects. Besides, LPS was co-precipitated with Lon by an anti-Lon antibody, showing the direct binding of LPS to Lon. These results suggest that LPS bound to Lon and inhibited the protease activity of Lon by inhibiting its ATPase activity. These results also seem to be another example of a negatively charged phosphate group in membrane components of Escherichia coli being involved in the regulation of protease activity of Lon through binding to Lon and inhibiting its ATPase activity, as in the case of cardiolipin.