Background: We examined the association of cardiorespiratory fitness and fatness with health complaints and health risk behaviors in 691 (323 girls) Spanish children aged 6 to 17.9. Methods: Health complaints and health risk behaviors were self-reported using items of the Health Behavior in School-aged Children questionnaire. Weight and height were measured and body mass index was computed. Cardiorespiratory fitness was measured by the 20-m shuttle-run test, and youth categorized as fit/unfit. Results: Unfit youth were more likely to report health complaints sometime (OR: 2.556, 95% CI: 1.299-5.031; and OR: 1.997, 95% CI: 1.162-3.433, respectively) and health risk behaviors such as drinking alcohol sometime (OR: 5.142, 95% CI: 1.214-21.783; and OR: 2.413, 95% CI: 1.484-3.923) than their fit counterparts. Overweight-obese youth were more likely to report health complaints (OR: 1.732, 95% CI: 1.019-2.945; and OR: 1.983, 95% CI: 1.083-3.629, respectively). The analysis of the combined influence of fitness and fatness revealed that fit youth had lower health complaints index than the fat-unfit and unfat-unfit groups (all P<.05). Conclusions: Low fitness and overweight-obesity increased the risk of having health complaints in youth, yet high levels of cardiorespiratory fitness might overcome deleterious effects of overweight-obesity on health complaints.