PURPOSE: To assess the impact of obesity and population attributes on the circadian pattern of cardiac autonomic modulation (CAM) in a population-based sample of adolescents. METHODS: We used data from 421 adolescents who completed the follow-up exam in the Penn State Children Cohort study. CAM was assessed by heart rate variability (HRV) analysis of beat-to-beat, normal R-R intervals from a 24-hour ECG, on a 30-minute basis. The HRV indices included frequency-domain (HF, LF, and LF/HF ratio) and time-domain (SDNN, RMSSD, and HR) variables. Nonlinear mixed-effect models were used to calculate a cosine periodic curve, each having three parameters quantifying its circadian period: M (mean levels of the HRV variables), A (amplitude of the oscillation), and theta (the time of the highest oscillation). RESULTS: The mean (SD) age was 16.9 (2.2) years, with 54 % male and 77 % white. The mean BMI percentile was 66, with 16 % obese (BMI percentile >/= 95). Overall, HF (a marker of parasympathetic modulation) gradually increased from the late afternoon, reached peak amplitude around 3 a.m., and then decreased throughout the daytime until late afternoon. In contrast, obesity had adverse effects on all circadian parameters. The age, sex and race showed varying differences on the CAM circadian parameters. The adjusted means (95 %Cls) of M, A, and theta for HF were 5.99 (5.79-6.19), 0.77 (0.66-0.89), 3:15 (2:15-4:15) a.m., and 6.21 (6.13-6.29), 0.66 (0.61-0.70), 2:45 (2:30-3:15) a.m. for obese and non-obese subjects, respectively. CONCLUSION: The circadian pattern of CAM can be quantified by the three cosine parameters. Obesity is associated with lower HRV even in young individuals like children/adolescents.