The separation of Pneumocystis carinii life-cycle stages while preserving infectivity is a hitherto unresolved challenge. We describe an original, reproducible, and efficient method for separating trophic from cystic forms of P. carinii using a high-speed cell sorter. The large amounts of highly purified (99.6+/-0.3%) infectious trophic and cystic forms can now be used to elucidate the poorly understood P. carinii life cycle.