Aims: The overall purpose of this study was to examine the relationship between motor proficiency and health-related fitness in children. In addition, the study aimed to determine if particular combinations of motor skills have a stronger relationship with individual health-related fitness measures. Methods: Seventy-seven children (F:28, M:49) (mean age: 11.19 +/- 2.74 years) participated in this prospective cohort study. Physical measures included the following: motor proficiency (Bruininks-Oseretsky Test of Motor Proficiency, Second Edition), bodymass index (BMI), waist circumference, blood pressure, heart rate and VO2 peak (mL/kg/min). Results: After factoring in age, motor proficiency as a combined total score had a strong negative relationship with the health-related fitness measures of BMI (r(2) = 0.62, P < 0.001) and waist circumference (r2 = 0.72, P < 0.001) and a strong positive relationship with VO(2)peak (r2 = 0.78, P = 0.002). Children with lower motor proficiency (<= 25th percentile) had a significantly larger mean waist circumference (M = 13.85 cm, 95% confidence interval (CI) (2.05, 25.66), P = 0.01), heavier weight (M = 22.17 kg, 95% CI (2.44, 41.91), P = 0.02) and higher BMI (M = 5.10 kg/m(2), 95% CI (0.33, 9.87), P = 0.03) than children with higher motor proficiency (<= 75th percentile). Conclusions: Motor proficiency, once corrected for age, is significantly related to a number of health-related measures in children and should therefore be considered a focus for investigation for children with poor health-related fitness (e.g. high BMI and waist circumference percentiles or low cardiorespiratory fitness), as motor incompetence could be an underlying contributing factor to a child's poor physical health.