Pneumocystis f. sp. hominis causes pneumonia in immunocompromised persons. In order to determine the types and distribution of P. carinii organisms within a single human lung, multiple samples were obtained from the lung of a child who died of P. carinii pneumonia. P. carinii DNA was detected in all of the samples and 2 different genotypes of P. carinii were identified, with uneven distribution in the lung, demonstrating that infection of the human lung is not necessarily clonal, and that different P. carinii genotypes may predominate in different areas of the lung.