This case-control study examines whether chronic diarrhea at initiation of antiretroviral therapy (ART) affects survival of human immunodefiency virus-infected patients. Cases (288) were treatment-naive, non-pregnant, adults with self report of frequent loose stool for > 3 weeks at the time ART was initiated. One-third of patients had an enteric pathogen identified including Cryptosporidium spp., Giardia spp., Isospora belli, Cyclospora cayetanensis, and Entamoeba histolytica. Control patients (400) did not have diarrhea when initiating ART. At six weeks, mortality was 10% in the patients with diarrhea and 5% in the patients without diarrhea (P = 0.009). Chronic diarrhea in patients requesting ART in Haiti is associated with increased early mortality.