The relationship between sleep duration and obesity in adolescents is inconclusive. This may stem from a more complex relationship between sleep and obesity than previously considered. Shifts towards evening preferences, later sleep-wake times, and irregular sleep-wake patterns are typical during adolescence but their relationship to body mass index has been relatively unexplored. This cross sectional study examined associations between sleep duration, midpoint of sleep, and social jetlag (estimated from seven days of continuous actigraphy monitoring) and morningness/eveningness with body mass indexes (BMI z scores) and waist to height ratios in 14 to 17 year old adolescents. Seventy participants were recruited from 9th and 10th grades at a public high school. Participant characteristics were as follows: 74% female, 75% post-pubertal, 36% Hispanic, 38% White, 22% Black, 4% Asian, and 64% free/reduced lunch participants with a mean age of 15.5 (SD, 0.7). Forty one percent of the participants were obese (BMI ≥ 95th percentile); 54% were abdominally obese (waist to height ratio ≥ 0.5). Multivariable general linear models were used to estimate the association between the independent variables (school night sleep duration, free night sleep duration, midpoint of sleep (corrected), social jetlag, and morningness/eveningness) and the dependent variables (BMI z scores and waist to height ratios). Social jetlag positively associated with BMI z scores (p < 0.01) and waist to height ratios (p = 0.01). Midpoint of sleep (corrected) positively associated with waist to height ratios (p = 0.01). After adjusting for social jetlag, school night sleep duration was not associated with waist to height ratios or BMI z scores. Morningness/eveningness did not moderate the association between sleep duration and BMI z scores. Findings from this study suggest that chronobiological approaches to preventing and treating obesity may be important for accelerating progress in reducing obesity rates in adolescents.