Background: Diarrhea is a major cause of morbidity and mortality among HIV-infected patients worldwide. Objective: We sought to determine the frequency of viral gastrointestinal infections among Brazilian HIV-infected patients with diarrhea. Methods: A collection of 90 fecal specimens from HIV-infected individuals with diarrhea, previously tested for the presence of bacteria and parasite was analyzed by polymerase chain reaction and sequence analysis for the presence of enteric viruses such as astrovirus, norovirus, rotavirus groups A, B and C, adenovirus, herpes simplex virus, Epstein-Barr virus, cytomegalovirus, and human bocavirus. Results: Twenty patients (22.2%; n = 90) were infected with parasites (11 single infections and nine coinfected with virus). Enteropathogenic bacteria were not found. Virus infections were detected in 28.9% (26/90) of the specimens. Cytomegalovirus was the most common virus detected (24.4%; 22/90). Coinfections with viruses and/or parasite were observed in 10 (11.1%) samples. Conclusion: Gastrointestinal virus infections were more frequent than parasitic or bacterial infections in this patient population.