Intervention strategies are crucial in planning school-based wellness programs. Understanding whether cardiovascular disease risk factors (RF) and self-perception of health (SPH) are affected by fitness or fatness can affect strategies. 865 girls and 497 boys were tested on body mass index (BMI), % body fat, triceps skinfold, waist girth (WG), systolic (Sp) and diastolic (Dp) blood pressure (mmHg), total cholesterol (C), physical inactivity (PI), cigarette smoking (S), SPH (self-reported health perception ranging from 1 to 9; 1 = lowest perception, 9 = highest), and maximal oxygen uptake (VO2) estimated from step test recovery heart rates. VO2 was used for fitness and WG for fatness in fitness v. fatness comparisons. Four groups of fitness and fatness were established for girls and boys, respectively, representing upper and lower 30th percentiles of VO2 and WG. Upper and lower 30th percentiles for VO2 were >36.3 and <32.2mlO2.kg.min (girls), and >50.9 and <42.5mlO2.kg.min (boys). Corresponding criteria for WG were >75.6 and <66.0cm (girls) and >78.7 and <70.5cm (boys). Differences in Sp, Dp, PI, C, S, and SPH were compared by ANOVA and Tukey between group multiple comparisons. Significant differences (P<0.05) were observed for girls in Sp, Dp and SPH. Means (SD) of SP, Dp and SPH, respectively, in the four groups were 111 (10), 74 (9), 5.2 (1) in high fit and high fat, 115 (9), 74 (9), 5.2 (1) in low fit and high fat, 107 (7), 67 (8), 6.0 (1) in high fit and low fat and 109 (11), 66 (6), 6.1 (1) in low fit and low fat. Significant differences in Sp and Dp were also observed for boys. Means (SD) of Sp and Dp, respectively, in the four groups were 119 (10), 73 (9) in high fit and high fat, 126 (11), 76 (11) in low fit and high fat, 111 (11), 68 (8) in high fit and low fat, 111 (12), 68 (9) in low fit and low fat. All significant differences in girls and boys were between levels of fatness regardless of fitness. Unlike girls SPH differences were not significant in boys. Data suggest that Sp and Dp in girls and boys are affected more by fatness than fitness. Significant differences in SPH between low and high fatness for girls but not boys, illustrates that low fatness girls perceive health more favorably compared with high fatness, regardless of their fitness. The information has application for intervention strategies.