Pneumocystis carinii pneumonia occurred in 6 of 17 rhesus monkeys infected with simian immunodeficiency virus and was studied by immunohistochemistry and by scanning and transmission electron microscopy. A monoclonal antibody/streptavidin-biotin-peroxidase staining method was highly sensitive for detecting the organisms in small, early lesions and was much more sensitive and specific than traditional silver impregnation methods. Reprocessing of paraffin wax-embedded lung tissue for scanning electron microscopy and use of a video printer to produce a photographic montage of light microscopic lesions allowed the same areas of tissue to be examined and compared by both methods. The ultrastructural morphology of P. carinii in the rhesus monkey was identical to that in man, as were the histological and electron microscopic lesions, including pulmonary fibrosis. Trophozoites were seen attached to alveolar type I epithelium mainly by intimate apposition to the plasma membrane, but scanning electron microscopy also showed attachment by elongated filopodia. Few macrophages were present in infected alveoli, and though phagocytosis followed by digestion of P. carinii trophozoites was observed, it appeared to occur at a very low level.