Brazil's National STD/AIDS Program is considered a model of success worldwide. However, AIDS-associated malnutrition continues in subgroups of Brazilian patients despite access to free highly active antiretroviral therapy (HAART). We aimed to identify the prevalence of malnutrition and associated factors among patients hospitalized with AIDS. Methods: We conducted a cross-sectional nutritional assessment among 127 adults hospitalized with AIDS in Brazil’s third largest city. Using anthropometric measurements, we determined the prevalence of malnutrition (body mass index ,18.5 kg/m2) at hospitalization. Prevalence ratios of malnutrition by demographic, socioeconomic, and clinical conditions were estimated using log-binomial regression. Results: One-third of participants were first informed of their HIV disease during the current hospitalization and recent treatment interruption was common (71%) among those on HAART. Forty-three percent were malnourished and 35% had severe weight loss at admission. Patient characteristics independently associated with malnutrition were older age (2% increased prevalence for each year; 95% confidence interval [CI] 0–4%) and very low daily per capita household income. Living on ,USD 2.00, USD 2.00–4.99 or USD 5.00–9.99 increased the prevalence of malnutrition by 2.01 (95% CI 1.06–3.81), 1.75 (95% CI 0.92–3.35) and 1.42 (95% CI 0.76–2.65) times, respectively, compared to $USD 10.00 per day. Chronic diarrhea was marginally associated with malnutrition (RR 1.42; 95% CI 0.99–2.04). Overall, 16% of the patients died during hospitalization. We observed a trend toward higher in-hospital case fatality among malnourished patients (22% vs. 12% for patients with and without malnutrition, respectively; chi square P = 0.14). Conclusions: Unacceptably high rates of malnutrition persist in Brazilians hospitalized with AIDS and our results reinforce the importance of nutritional evaluations in these patients. Improved early testing and treatment adherence strategies may continue to help reduce AIDS-related morbidity and mortality in Brazil, yet novel interventions to disrupt the cycle of poverty, HIV, and malnutrition are also urgently needed.