Enteroparasites are related to gastrointestinal alterations among patients with HIV/AIDS, some causing severe manifestations in the period before the institution of the highly active antiretroviral therapy (HAART). The prevalence of enteroparasitoses in patients with HIV/AIDS seen at two hospitals in Ceará , Brazil, was compared in the pre-HAART (Group 1; n = 482) and HAART (Group 2; n = 100) eras. Fecal parasitologic examinations (FPE) were performed using the direct, Lutz, Baermann-Moraes and modified Ziehl-Neelsen methods. The following parasites were detected in Groups 1 and 2, respectively: Strongyloides stercoralis - 30.1% and 11% (p<0.0001), Ascaris lumbricoides - 15.6% and 2% (p<0.0001), hookworms - 13.7% and 2% (p<0.0001), Trichuris trichiura - 13.1% and 1% (p<0.0001), Hymenolepis nana - 0 and 1% (p = 0.1718), Giardia duodenalis - 7.9% and 1% (p = 0.0076), Entamoeba histolytica/dispar - 3.3% and 1% (p = 0.3301), Isospora belli - 4.8% and 1% (p = 0.0993), Cryptosporidium sp. - 8.1% and 0 (p = 0.0007), and non-pathogenic protozoans as well. There was a significant reduction in the prevalence of enteroparasites between the eras (63.9% to 24%; p<0.0001). In the HAART era, the following observations were made: greater frequency of enteroparasites in patients without antiretroviral therapy (p = 0.0575), as in those with AIDS (p = 0.08), and diarrhea (36% of the patients); lack of association with positive FPE (p = 0.626); and non-detection of Cryptosporidium sp. Strongyloides stercoralis showed an elevated prevalence in the two eras and was more frequent in men (32.41%) than women (19.04%) of Group 1 (p = 0.018), a finding suggesting the transmission of the helminth through sodomy. The advent of the HAART modified the profile of opportunistic infections, including parasites, probably due to the reconstitution of cellular immunity and the direct action of HAART on the parasites.