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We determined the degree to which variation in cardiac autonomic modulation was explained by race, sex, moderate-vigorous physical activity (MVPA), cardiovascular fitness (CVF), percent body fat (%BF), waist girth, subcutaneous abdominal adipose tissue (SAAT), and visceral adipose tissue (VAT).Subjects were 304 adolescents; SAAT and VAT values were available for 168 youths. Cardiac parasympathetic modulation (PM) was the root mean square of successive differences (RMSSD). Sympathetic-parasympathetic balance was the ratio of low- to high-frequency power (LFnu:HFnu). MVPA was measured with accelerometry, CVF with a treadmill, %BF with dual-energy x-ray absorptiometry (DXA), and SAAT and VAT with magnetic resonance imaging (MRI).Root mean square of successive differences was higher, and LFnu:HFnu was lower, in blacks than in whites. The final regression model revealed positive relations with CVF and MVPA, and a %BF by race by sex interaction, such that higher %BF was associated with lower RMSSD in black females and higher RMSSD in white females. Higher RMSSD was associated with lower VAT; for SAAT, the relationship was negative for blacks and positive for whites. For LFnu:Hfnu, a negative relationship was seen with MVPA and higher waist girth was associated with a higher ratio in blacks, but not in whites. Both higher VAT and SAAT were related to higher LFnu:HFnu.Black youths had a more favorable HRV profile than white youths. After controlling for age, race, and sex, more favorable HRV profiles were associated with more MVPA, better CVF, and less visceral and subcutaneous adiposity. The deleterious impact of higher adiposity was greater in blacks, especially females, than in whites. Enhancement of cardiac autonomic modulation may be a pathway through which physical activity, fitness, and leanness contribute to cardiovascular health early in life.