Chronic disease is related to poor diet quality. The Healthy Eating Index (HEI) was developed to assess diet quality. The Youth HEI (YHEI) is an adaptation of the HEI for use with children and adolescents. The objectives were to compare HEI and YHEI scores among adolescents at risk for chronic disease and to compare associations between the scores and health indicators. This cross-sectional study included 2 low-income, urban African American adolescent samples (Challenge, n = 196; Three Generation, n = 121). HEI and YHEI scores were calculated from a FFQ and compared with BMI, body composition, and micronutrient, energy, and dietary intakes. YHEI scores were lower than HEI scores across both adolescent samples (Challenge, 48.94 +/- 9.31 vs. 62.83 +/- 11.75; Three Generation, 47.08 +/- 9.65 vs. 59.93 +/- 11.27; P < 0.001). Females (64.47 +/- 11.70) had higher HEI scores than males (61.15 +/- 11.61) (P < 0.05), but there was no gender difference in YHEI scores. HEI and YHEI scores were associated with higher micronutrient and total energy intakes (r = 0.19-0.76; P < 0.05). Higher percent body/abdominal fat was associated with lower HEI scores (r = -0.17 to -0.19; P < 0.05) but not with YHEI scores. BMI was not associated with either HEI or YHEI scores. In conclusion, many adolescents were consuming diets that placed them at risk for developing chronic disease. Although both the HEI and YHEI are useful in assessing diet quality, the HEI is inversely associated with body composition, a predictor of chronic disease, and accounts for gender differences in the Dietary Guidelines, whereas the YHEI discounts nutrient-poor, energy-dense foods.