Acidithiobacillus ferrooxidans cells grown in ferrous ions were used to study the surface modification of pyrite and chalcopyrite, with focus on coagulation of very fine particles (-5 m). The zeta-potential studies of the minerals, before and after bacterial treatment, showed that the cells have a distinct influence on the surface charge of pyrite and chalcopyrite. The maximum coagulation of particles determined by Turbiscan as a function of pH correlated well with the zetapotential results. Using diffuse reflectance FT-IR spectroscopic studies, the adhesion of cells showed a varied influence on these minerals. The results demonstrate that Acidithiobacillus ferrooxidans interact with pyrite and chalcopyrite differently, allowing selective coagulation of one mineral from the other under different pH conditions.