Human immunodeficiency virus (HIV) infection has altered both the epidemiology and outcome of enteric opportunistic parasitic infections. This study was done to determine the prevalence and species/genotypes of intestinal coccidian and microsporidial infections among HIV/AIDS patients with diarrhea and/or a history of diarrhea alternately with an asymptomatic interval, and their association with ART therapy. This cross sectional study was done from May 2015 to March 2018 in IGIMS, Patna. Sociodemographic data and a history of diarrhea were collected by interviewing 234 HIV patients ( 146 males and 94 females).Using routine microscopy, trichrome staining, modified ZN staining incidence of coccidian parasites were found to be as Cryptosporidium 21.8% , followed by Strongyloides 17.6%, microsporidia, Isospors, Giardia, Trichuris, and taenea. ART treatment was significantly associated with the decline of opportunistic parasites and diarrhea (p < 0.05) while no ART had relatively greater incidence of opportunistic intestinal parasites.