Microsporidia infects immunocompromised populations such as human immunodeficiency virus(HIV)-positive patients, causing diarrhea and other life-threatening symptoms. Few studies on this infection have been conducted in China. This study collected 22 HIV-positive patients in Chongqing, who have not received antiviral treatment. The immune profile analysis of these 22 patients showed the average lymphocytes were 0.93±0.13×10⁹/L, CD4^＋T cells were 132±22 cells/mL, CD8^＋T cells were 495±91 cells/mL, and CD4/CD8 ratio was 0.37±0.1, indicating all the patients were immunocompromised, thus vulnerable to opportunistic infections. The total DNA was extracted from the respective stool samples. The existence of microsporidia was confirmed by PCR and DNA sequencing. The results showed that the infection rate was 36.3% (8/22), and caused by Encephalitozoon spp, mainly E. hellem and E. intestinalis. Further comparison between Encephalitozoon spp infected and un-infected patients showed that, lymphocytes were 0.51±0.1 vs 1.17±0.17×10⁹/L, P<0.05; CD4⁺T cells were 71±27 vs 167±28 cells/ mL, P<0.05; CD8^＋T cells were 209±35 vs 658±123 cells/ mL, P<0.05, suggesting the infected patients were severely immune-suppressed. The current study is the first investigation of microsporidia infection in HIV-positive patients in Chongqing area. It demonstrates the correlation between immune-suppression and microsporidia infection, and the high infection rate of Encephalitozoon spp in Chongqing area. Together, this provides evidence to elucidate the mechanisms of microsporidia-host interactions, as well as insights into public health control.