The association of Merkel cell polyomavirus (MCPV) with Merkel cell carcinoma (MCC) in immunocompromised individuals has been revealed in a number of surveys. The study of MCPV specific antibody titers and viral loads in such patients has a great attraction for research groups interested in viral reactivation. In this cross-sectional study to evaluate MCPV antibody titer， DNA prevalence and viral load in peripheral blood mononuclear cells (PBMCs)， we examined 205 HIV-1 infected patients and 100 un-infected controls. The HIV-1 infected patients divided into two groups (HIV/AIDS and non-AIDS) according to their CD4 status. Total IgG antibody titer against MCPV was analyzed by virus like particle (VLP)-based enzyme linked immunosorbent assay (ELISA). Presence of MCPV-DNA in subject's PBMCs was examined by quantitative real-time PCR assay. Levels of anti-MCPV IgG in HIV/AIDS patients were significantly higher than those in non-AIDS HIV-infected and control subjects (p value = <0.001). The prevalence rate of MCPV-DNA in PBMCs of HIV/AIDS， non-AIDS HIV-infected and un-infected controls were 17%， 16%， and 14% respectively. The MCPV viral load among the groups ranged between 0.15 to 2.9 copies/10cells (median， 1.9 copies/10cells)， with no significant difference between the studied populations (p value = 0.3).