Pneumocystis jirovecii is an important opportunistic agent leading to pneumonia in immunocompromised patients. In this study, the presence of P.jirovecii were investigated by using Giemsa stain, indirect fluorescent antibody (IFA) test and two different nested polymerase chain reaction (nPCR) assays in respiratory samples obtained from 50 immunocompromised patients presenting with respiratory symptoms. The target genes used for nested PCR were mitochondrial large subunit ribosomal RNA (MtLSUrRNA) and internal transcribed spacer (ITS) region. P.jirovecii was detected in 7 (14%) and 11(22%) respiratory samples by IPA and PCR, respectively, although all samples were negative with Giemsa stain. As a result, IFA and PCR were found to be rapid and reliable tests for the diagnosis of P.jirovecii infections and they should better be used together for accurate diagnosis.