The emerging protozoan parasites Cryptosporidium, Cyclospora cayetanensis and Isospora belli have altered the etiological spectrum of diarrhea. The progressive decline in CD4 cell count in AIDS patients and lack of active immunity in the face of exposure to contaminated food and water in young children make these groups of persons particularly susceptible to protracted and severe diarrhea caused by the above parasites. Cryptosporidiosis is caused by human as well as several zoonotic species. The present study was undertaken to examine the prevalence of Cryptosporidium species, C. cayetanensis and I .belli among these two susceptible populations in comparison with adult immunocompetent individuals with diarrhea and to identify the Cryptosporidium species prevalent in these populations. A total of 447 children under the age of 5 years, 175 HIV-seropositive adults and 200 HIV seronegative adults with diarrhea attending tertiary care hospitals located in the twin cities of Secunderabad and Hyderabad in South India were included in the study. Single fecal samples were collected. Wet mounts and modified Ziehl Neelsen stained smears made from concentrated fecal specimens were screened microscopically for oocysts of Cryptosporidium, Cyclospora cayetanensis and Isospora belli. DNA extracted from fecal samples positive for Cryptosporidium was subjected to PCR RFLP for species identification. Cryptosporidium was detected in all the three groups, I.e. children (8.7%), HIV-seropositive adults (6.85%), and HIV-seronegative adults (1%). Isospora and Cyclospora were detected only among HIV- seropositive persons at a frequency of 16% and 1% respectively. C. hominis (71.7%) and C. parvum (18.9%) were the only 2 species of Cryptosporidium detected.