The physical structures of lipid layers on pyrite (FeS2), a ubiquitous sulfide mineral, were studied in air and in water by atomic force microscopy (AFM). Egg PC, a phospholipid that forms bilayer structures on atomically flat substrates, was investigated, and our experimental observations show that this lipid formed bilayers on an atomically rough pyrite surface, as inferred by a measured layer thickness of 5.0 +/- 0.2 nm. The surface coverage of the lipid coating increased from approximately 15% to 80% when the concentration of the lipid suspension was increased from 0.014 to 0.15 mM. Although further increases up to 1.5 mM resulted in an incremental increase in surface coverage of only 5%, multilayer structures of 20- to 40-nm height formed on top of the first bilayer. The findings provide a structural explanation for the results of earlier kinetic studies showing that the presence of the lipid decreases the rate of pyrite oxidation in air and in water. Lipid coatings applied to iron-sulfide bearing minerals are a possible approach to preventing oxidation and acidification and thereby mitigating environmental damage that can result from acid mine drainage.