Background: Children with SLE are known to have higher fat mass compared to their peers but there are no published data regarding exercise capacity as measured by cardiovascular endurance and muscle strength. In our pilot study of ten children with SLE, we sought to examine body composition, cardiovascular endurance, and isometric muscle strength. Findings: Ten pediatric SLE patients were studied with a mean age of 15.5 years and 90 % female. Percent body fat above 30 %, the recommended normal level in adolescent females, were found in 89 % of female subjects and 40 % of all participants had lower than the recommended norms of muscle mass for their age/gender. Subjects with renal disease were more likely to have low muscle mass compared to those without renal disease (p = 0.03). Cardiovascular endurance was reported as estimated maximal oxygen consumption (VO2max) during cycle ergometry. All participants scored in less than fifth percentile for VO2max measurements compared to data from age and gender matched published norms. Isokinetic muscle strength testing was performed on upper and lower extremities. Only one participant (male subject) reached goal percentiles for age and gender. Conclusions: We found significant deficit in body composition, muscle strength and cardiovascular endurance in the pediatric SLE population compared to reported published norms. Clinicians should consider these data and focus on exercise programs that can increase aerobic capacity and muscle strength in this high-risk population.