Introduction: Pneumocystis pneumonia (PCP) remains a serious cause of sickness and death in immunocompromised patients. Lung injury and respiratory impairment during pneumocystis pneumonia are mediated by marked inflammatory responses in the host to the organism. Quantitative PCR (qPCR) is more sensitive than microscopy for detecting Pj in BAL. The relevant threshold remains to be determined and may vary according to the underlying disease. Methods: All BAL samples were obtained from immunocompromised and non-immunocompromised patients presenting with respiratory symptoms referred to the Department of infectious diseases of Alzahra Hospital, Isfahan, Iran. All statistical analyses were performed using SPSS (Statistical Package for the Social Sciences, Chicago, IL, USA) version 22. Results: 2 patients (12%) of immunocompromised patients were positive for Pj. Among nonimmunocompromised patients, 3 (8%) were positive for Pj. Fisher exact test demonstrated that Pj positivity was not significantly different between the two groups. The overall frequency of Pj positivity was estimated as 10%. Conclusion: 12% of immunocompromised patients and 8% of non-immunocompromised were colonized by Pj which may progress to PJP or contaminate susceptible individuals.