Intestinal parasites in HIV infected patients are a compelling issue in epidemiological settings with high prevalence of these parasites. The present study reviewed frequencies of diagnosis for common intestinal parasites in HIV infected patients in association with sex, age, HIV risk behavior and CD4 lymphocyte count. Patients with confirmed HIV diagnosis and positive routine stool examination between January and December 2000 were selected. Diagnostic methods for Cyclospora cayetanensis and microsporidia were not included in the routine stool examination. A total of 146 patients had one or more positive samples (median 1.5) with age ranging between 2-75 years (mean: 34). Most of them were male (70.5%) and 53.6% had a CD4 count > 200 cells/mm³ (median: 158.5 cells/mm³). Endolimax nana (27.4%), Entamoeba coli (22.6%), Strongyloides stercoralis (21.9%), Giardia lamblia (13.0%), Isospora belli (12.3%), Ascaris lumbricoides (8.2%), Cryptosporidium parvum (6.8%) were the most frequent parasites diagnosed in this group. G. lamblia was more common in children with vertically transmitted HIV and men who have sex with men. No significant associations were found in relation to sex and age. Patients with CD4 count < 200 cells/mm³ presented lower prevalence of non-pathogenic parasites (e.g. E. nana OR 0.46 and E. coli OR 0.33) but had more pathogenic parasites diagnosed such as S. stercoralis (OR 3,9) and I. belli (OR 3,5) in relation to those HIV-infected individuals with CD4 count e 200 cells/mm³. These results underscore the importance of S. stercoralis in AIDS patients; the decrease in C. parvum prevalence in relation to previous reports from our institution before the routine use of HAART; local differences in parasite profiles in comparison to other epidemiological settings as well as changes in the proportion of diagnosis for pathogenic and non-pathogenic parasites according to the immune compromise due to HIV infection