Six pathogenic strains of Naegleria fowleri, two of Acanthamoeba castellanii, and three of Acanthamoeba polyphaga were tested in vitro for susceptibility to a variety of potentially useful therapeutic agents. Minimal motility inhibitory concentrations and minimal inhibitory concentrations were determined by a technique of subculturing pure clones of amoebae in plastic tissue culture chamber slides containing liquid axenic media and serially diluted drug, incubating at 30 degrees C for Acanthamoeba and at 37 degrees C for Naegleria, and observing on an inverted microscope at 6 h for inhibition of motility and at 24 and 48 h for inhibition of growth. Drug concentrations were selected on the basis of fluid levels achievable in humans. Amphotericin B, clotrimazole, and miconazole were the most effective drugs against Naegleria, whereas polymyxin B sulfate and pentamidine isethionate were somewhat effective against pathogenic Acanthamoeba. Our results suggest that amphotericin B is the most effective agent against Naegleria, but few agents are effective against Acanthamoeba.