Parasites are important enteric pathogens among patients with human immunodeficiency virus (HIV) infection. There have been very few reports on the prevalence of intestinal parasites among such patients in Iran. To determine the prevalence of intestinal parasites among HIV-positive individuals, we collected single stool samples and analyzed them for detection of various intestinal parasites from 206 HIV-positive individuals with different immune status visited in different medical centers in Iran. The data were tested for statistical significance with chi(2) and Mann-Whitney U tests. The overall prevalence of intestinal parasites was 18.4% (95%CI: 13.7, 24.3). More specifically, the following parasites were identified: Giardia lamblia (7.3%), Blastocystis hominis (4.4%), Entamoeba coli (3.9%), and Cryptosporidium parvum (1.5%). Other parasites observed included Strongyloides stercoralis and Hymenolepis nana in two cases and Dicrocoelium dendriticum in one. Of the 38 patients who tested positive for intestinal parasites, 15 (39.2%) had diarrhea. Intestinal parasites were significantly more common among patients with diarrhea than those without (P < 0.001). Further, CD4 counts were significantly lower among individuals with diarrhea than those without (P < 0.001). This study highlights the importance of testing for intestinal parasites among Iranian HIV-positive patients, especially those with low immunity presenting with diarrhea.