Pneumocystis carinii pneumonia (PCP) remains the most common opportunistic infection among human immunodeficiency virus-infected persons. Despite this, little is known concerning the transmission dynamics of this infection. In the absence of a reliable method to isolate and culture P. carinii from environmental samples, it has not been possible to assess the importance of person-to-person transmission in the epidemiology of PCP. A molecular viability assay was developed for the human form of P. carinii (P. carinii f sp hominis) that is applicable to both clinical specimens and environmental samples. This assay will enable the evaluation of the spread and persistence of viable human P. carinii in the environment.