Few studies have evaluated habitual nutrient intake among HIV-infected youth in the United States, even though diet may influence disease progression and risk of comorbidities. This study determined habitual micronutrient and macronutrient intake in HIV-infected youth. HIV-infected subjects and healthy controls 1-25 years old were prospectively enrolled. Nutrient intake was assessed via 24-h dietary recalls performed every 3 months for 1 year and compared to recommended intake from the U.S. Dietary Reference Intakes (DRIs) and Acceptable Macronutrient Distribution Ranges (AMDRs). Subjects with two or more food recalls were analyzed (175 HIV(+) and 43 healthy controls). Groups were similar in age, race, sex, body mass index, and kilocalorie intake. In both groups, intake of several micronutrients was below the DRI. In addition, HIV(+) subjects had a lower percentage DRI than controls for vitamins A, D, E, pantothenic acid, magnesium, calcium, folate, and potassium. HIV(+) subjects' percentage caloric intake from fat was above the AMDR and was higher than controls. Caloric intake was negatively correlated with current and nadir CD4 count. Zinc, riboflavin, and magnesium percentage DRI were positively associated with current CD4 count. In HIV(+) subjects not on antiretroviral therapy, HIV-1 RNA levels were negatively correlated with protein intake. HIV(+) youth have an inadequate dietary intake of several essential nutrients and poorer dietary intake compared to controls. Intake of some nutrients was associated with important HIV-related factors. Further investigation is warranted to determine the impact of dietary intake of specific nutrients on HIV progression and chronic complication risk in this population.