Since the beginning of the AIDS pandemic, opportunistic infections have been recognized as common complications of HIV infection. Enteric protozoan parasitic infections are one of the leading causes of morbidity and mortality in HIV infected patients. The present study is, therefore, aimed to determine the prevalence of these parasites and study their association with immune status in HIV patients with emphasis on the correlation between various diagnostic techniques to give an accurate diagnosis to avoid empirical treatment. This prospective study, carried out between November 2009 and May 2010 included all HIV seropositive patients presenting with diarrhea to the ART center. A total of 64 stool samples were analyzed by wet mount examination, three different staining techniques, and antigen detection by ELISA for various enteric protozoan infections. Total prevalence of enteric protozoan parasites was 30%. Among the total cases, Cryptosporidium was seen in 12% cases followed by Giardia, E. histolytica and Isospora belli. The maximum diagnostic yield for coccidian parasites was with safranin-methylene blue staining technique. Parasitic burden contributes towards early morbidity in HIV infection. This study provides important information about prevalence of intestinal protozoan parasites in HIV infection. A combination of procedures should be carried out for the screening of stool specimens of HIV patients for better diagnosis and management.