Reports suggest children with high aerobic fitness (VO2max; mL/kg/min) have healthier profiles of TNF-α and IL-6; however, research has not accounted for differences in adiposity between high-fit and low-fit individuals. Thus, this study examined differences in inflammatory markers of obese and normal weight children of different fitness levels, using two different VO2max units: per unit of fat free mass (VO2FFM) or total body mass (VO2kg). Children (n = 124; ages 8-12) were divided into four matched groups; normal weight high-fit (NH), normal weight lowfit (NL), obese high-fit (OH), and obese low-fit (OL). Height, weight, skinfolds, body mass index (BMI), and predicted VO2max were measured and a morning, fasting blood sample taken. IL-6 was elevated in the NL and OL groups compared with the NH group, as well as the OL group compared with the OH group. No differences were found in TNF-α. The relationship between IL-6 or TNF-α and the two units of predicted VO2max did not differ suggesting that either VO2FFM or VO2kg can be used to describe aerobic power when studying inflammation and exercise in youth. The relationship between IL-6 or TNF-α and predicted VO2max, whether expressed per mass or per fat-free mass was similar, suggesting that both can be used to describe aerobic power when studying inflammation and exercise in youth. Given the polar design of this study, this relationship should be confirmed including overweight subjects.