Microsporidia are emerging pathogens which cause an opportunistic infections in immunocompromised patients, especially those with AIDS. Intestinal microsporidiosis is the most recognized infection, whereas urinary tract infections caused by microsporidia are rarely paid attention to either due to their subclinical course or diagnostic difficulties. In this report dual microsporidial infection of urinary tract, caused by Enterocytozoon bieneusi and Encephalitozoon cuniculi was described in HIV/AIDS patients under cART therapy. Since microsporidiosis can cause severe complications or even death in immunosuppressed patients, our results suggest that microsporidial infection should be included in routine investigation of HIV-positive patients, even asymptomatic.