The diagnosis of Pneumocystis jirovecii pneumonia (PJP) is mainly based on microscopic detection of P. jirovecii in the respiratory samples. Quantitative PCR (qPCR) can detect low levels of P. jirovecii DNA but cannot differentiate between infection and colonization. Therefore a new and more accurate assay have to be used. 1,3 BDglucan (BD-glucan) with a threshold value of 100 pg/ml can differentiate P. jirovecii infection from colonization. Aim The aim of this study is to evaluate the diagnostic accuracy of qPCR and BD-glucan assays in differentiating pneumocystis infection from colonization in immunocompromised patients with help of radiological pulmonary infiltrates. Patients and methods This study consisted of 75 immunocompromised patients (37 renal transplanted patients and 38 HIV patients) who were admitted for radiological pulmonary infiltrates and who presented a clinical picture suspecting PJP. They were investigated using microscopic staining of their respiratory samples (induced sputum or bronchoalveolar lavage).By applying both qPCR and serum BD-glucan assays we can differentiate between P. jirovecii infection from colonization. Results In this study, the first group of 25 patients were diagnosed as definite PJP, the second group of 20 patients were diagnosed as having pneumonia with P. jirovecii colonization, and a third group of 30 patients were diagnosed as having pneumonia without colonization. The number of copies of fungal DNA detected by qPCR were significantly higher in a definite PJP than in those with pneumonia accompanied with P. jirovecii colonization. Also BD-glucan assays were significantly higher in definite PJP by applying a threshold value of 100 pg/ml. The sensitivity and specificity of qPCR for differentiation of PJP infection from colonization were 100 and 64%, respectively, whereas the sensitivity and specificity of BD-glucan were 100 and 96%, respectively. Conclusion Both BD-glucan and qPCR assays had high diagnostic values in differentiating definite PJP from P. jirovecii colonization, and by applying qPCR with two cutoff values combined with serum BD-glucan using a threshold value of 100 pg/ml. Egypt J Bronchol 2018 12:467–472 © 2018 Egyptian Journal of Bronchology Egyptian Journal of Bronchology 2018 12:467–472 Keywords: colonization, immunocompromised host, Pneumocystis jirovecii pneumonia, quantitative PCR, BD-glucan, respiratory tract infection aChest Department, bTropical Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt Correspondence toAmal Abd Elazeem Sadon, MD, Al-Sharkia Government, Faqus, Al Zeraaeen Building, 44511, Egypt. Tel: +20 111 868 6807; e-mail: amalsadon@yahoo.com