Antigenic sites on Pneumocystis carinii, the basis for organism enumeration by an enzyme-linked immunosorbent assay (ELISA) were adversely affected by incubation in detergents. However, stronger detergent concentrations were needed to eliminate high levels of non-specific background. Good P. carinii quantification was obtained with low non-specific background when the detergent was used only in the washing steps and not in cell suspension solutions. Formalin fixation of the cells resulted in good ELISA quantification of organism numbers with low non-specific background. No adverse effects were observed using a detergent on fixed cells. Although the system's range of accuracy needs to be expanded, a reduction in the number of organisms in response to the effects of pentamidine in vitro could be demonstrated by ELISA.