Objective:To investigate the infection rate of pneumocystis carinii(PC) in human immunodeficiency virus(HIV) negative immunocompromised patients in Chongqing in order to provide biological references for its early diagnosis and treatment. Methods:Sputum specimens were collected from 71 HIV-negative immunocompromised patients in Chongqing and were detected by Gomori’s methenamine silver stained(GMS) and internal transcribed spacer(ITS)-nested PCR,respectively. Results:PC was detected out in two cases out of 71 cases by GMS and PC was detected out in 25 cases by nested PCR,the difference between the two methods were significant(?字2=21.04,P=0.000) .There was no significant difference in infection rate between difference genders( ?字2=0.375,P=0.540) and different ages(?字2=0.777,P=0.678). The infection rates of patients with cancer,heamatolagic disorder,kidney transplantation,liver transplantation and connective tissue disease were 33.33%,26.67%,40.00%,42.86% and 39.13% respectively. There was no signifi-cant difference in infection rates between the different case groups(P=0.897). The infection rate was significantly higher than that of abroad report and was the same as that of domestic report in 2009. Conclusion:The infection rate of PC of HIV-negative immuno-compromised patients in Chongqing is high. Clinician should enhance the alertness of patients with PC.