This study investigated whether heart rate variability (HRV) in young African-Americans differed from that in young European Americans. It further examined the genetic and/or environmental sources of HRV variance and to what extent they depend on ethnicity or gender in young twins. Subjects were available from 1 data set including 166 subjects (mean age 16 +/- 2 years; 63 African-Americans) and another including 219 twins (11 singletons [4 African-Americans] and 104 pairs [42 African-Americans]; mean age 15 +/- 2 years). HRV was measured over 256 RR intervals in a supine position. Two time-domain variables, the SD of normal RR intervals (SDNN) and the root-mean-square of successive differences (RMSSD) of normal RR intervals, and 3 frequency-domain variables, high-frequency (HF) power, low-frequency (LF) power, and the LF power/HF power ratio, were used. African-Americans had higher RMSSDs (p <0.01) and HF power (p = 0.047) and lower LF power/HF power ratios (p <0.01) than European Americans. These differences remained significant after adjusting for covariates. All HRV parameters were heritable; estimated heritability ranged from 32% to 71%. Model fitting showed no ethnic or gender differences for any measure. SDNN, RMSSD, and HF power were strongly correlated (r values >0.8). One factor explaining >90% of the variance for all 3 measures was identified. The heritability of this combined HRV score was 70%. In conclusion, this study suggests that ethnic differences in HRV already exist in youth, with African-Americans having greater HRV than European Americans. High heritability estimates for HRV measures were observed, and no differences in HRV heritability estimates were noted for ethnicity or gender.