Lysosomotropic agents have antitumor, antifungal and antimicrobial properties. These small, amphiphilic compounds, as weak bases, readily penetrate the lipid bilayer and diffuse into acidic subcellular compartments such as lysosomes or vacuoles. The mechanism of action of lysosomotropic compounds can be distinct, depending on their chemical structure and/or the kind of cells influenced. Our investigations of the influence of lysosomotropic agents on Saccharomyces cerevisiae have lead to a partial explanation of their mechanism of action. The amphiphilic character enables the compounds to penetrate the lipid bilayer and disturb its structure and functions and can inhibit the activity of plasma membrane H+ATPase. The accumulation of the compounds in yeast vacuoles, disrupting them and killing yeast cells, is another mechanism of action. Lysosomotropic agents can be substrates for ABC transporters in Saccharomyces cerevisiae cells.