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The incidence of disseminated Mycobacterium avium complex (MAC) infection in HIV patients has fallen markedly since the introduction of effective antiretroviral therapy (ART). However, current guidelines still recommend primary prophylaxis. We conducted a retrospective cohort study in a university-affiliated hospital from January 1998 to January 2014. During that period, HIV patients who had at least one CD4 cell count below 50 cells/mm3 and had been treated with ART were enrolled. We compared incidence of disseminated MAC infection in the 12 months after the first CD4 cell count below 50 cells/mm3 between prophylaxis and nonprophylaxis groups. A total of 157 patients were enrolled and the total observation period was 144 patient-years (PY). Thirty-three patients (21%) received primary MAC prophylaxis. The initial CD4 cell count of the prophylaxis group was lower than that of the nonprophylaxis group (P = 0.024), but the proportion of patients who reached a CD4 cell count >100 cells/mm3 (P = 0.234) and were virologically suppressed (P = 0.513) 12 months after ART commencement was not different in the prophylaxis and nonprophylaxis groups. The incidence of MAC did not differ significantly between the groups (3.4/100 PY versus 0.8/100 PY, P = 0.368). Routine MAC prophylaxis may be not required in the era of effective ART.