Historically, Pneumocystis carinii pneumonia has been the most frequent cause of morbidity and mortality in patients with AIDS. Antiprotozoan drugs are effective in the treatment and prophylaxis of P. carinii pneumonia, which lends credence to the widely held view that P. carinii is a protozoan. However, recent genetic evidence suggests that P. carinii should be classified as a fungus. Translation elongation factor 3 (EF-3) is an essential, soluble translation component which is unique to fungal protein synthesis and is not required for protein synthesis in other eukaryotes. We have identified and isolated a gene for EF-3 from P. carinii, adding more evidence for this organism's assignment as a fungus.