Pneumocystis pneumonia (PCP) is a major cause of morbidity and mortality among immunocompromised persons, and it remains a leading acquired immune deficiency syndrome (AIDS)-defining opportunistic infection in human immunodeficiency virus (HIV)-infected individuals throughout the world. Pneumocystis has proven difficult to study, in part due to the lack of a reliable culture system for the organism. With the development of molecular techniques, significant advances in our understanding of the organism and the disease have been made over the past several years. These advances include an improved understanding of host-organism interactions and host defense, the development of noninvasive polymerase chain reaction (PCR)-based diagnostic assays, and the emerging data regarding the possible development of trimethoprim-sulfamethoxazole-resistant Pneumocystis. In addition, the recognition that patients without PCP may nevertheless be carriers of or colonized with Pneumocystis, and observations that suggest a role for Pneumocystis in the progression of pulmonary disease, combine to signal the need for a comprehensive and accessible review. In May 2005, the American Thoracic Society sponsored a one-day workshop, "Recent Advances and Future Directions in Pneumocystis Pneumonia (PCP)," which brought together 45 Pneumocystis researchers. The workshop included 21 presentations on diverse topics, which are summarized in this report. The workshop participants identified priorities for future research, which are summarized in this document.