Autonomic cardiac function can be indirectly detected non-invasively by measuring the variation in microtiming of heart beats by a method known as heart rate variability (HRV). Aerobic training for sport is associated with reduced risk for some factors associated with cardiovascular diseases (CVD), but effects on autonomic function in different athlete types are less known.To compare cardiac autonomic modulation using a standard protocol and established CVD risk factors in highly trained intercollegiate athletes competing in aerobic, explosive, and cross-trained sports. A total of 176 college athletes were categorized in distinct sports as explosive (EA), aerobic (AA), or cross-trained (mixed) athletes. Eight different HRV measures obtained at rest were compared across training type and five health factors: systolic (SBP), diastolic blood pressure (DBP), body weight (BW), sex, and race. All athletic types shared favorable HRV measures that correlated with low CVD risk factors and indicated normal sympathovagal balance. A significant correlation was reported between DBP and pNN50 (% RR intervals > 50 ms) (β = −0.214, p = 0.011) and between BW and low-frequency (LF) power (β = 0.205, p = 0.006). Caucasian and African American athletes differed significantly (p < 0.05) with respect to four HRV variables: pNN50, HF power, LF power, and LF/HF ratios. Explosive, aerobic and mixed athletes had similar cardiovascular and autonomic HRV results in all eight HRV parameters measured. All athletes reported LF and pNN50 values that were significantly correlated with two CVD risk factors: DBP and BW. Compared with Caucasian teammates, African American athletes demonstrated lower LF/HF and higher pNN50, indicating an even more favorable resting sympathovagal activity and healthy CV function.