We developed a rapid, yet efficient procedure for extracting DNA from respiratory specimens, and a user friendly ELISA format PCR product detection assay. By combining these two technologies we were able to perform, in a diagnostic laboratory, a prospective evaluation of PCR as a method for diagnosing Pneumocystis carinii pneumonia (PCP). The results of this study indicate that the use of PCR could improve the efficiency of diagnosis of PCP, especially from non-invasive specimens (induced sputa). The improvement in diagnosis effected by PCR was particularly marked in patients that, a priori, might be expected to produce sputum specimens containing a low number of organisms (for example HIV patients receiving chemoprophylaxis, immunosuppressed non HIV patients).