Purpose To investigate whether body mass index (BMI) percentile impacts the morphology of the capital femoral epiphysis in children and adolescents without hip disorders. Methods We assessed 68 subjects with healthy hips who underwent a pelvic CT for evaluation of appendicitis. There were 32 male patients (47%) and the mean age was 11.6 years (sd 2.3). The BMI (k/m2) was calculated for sex- and age-related percentiles according to the Centers for Disease Control and Prevention growth charts. CT images were segmented, and the epiphysis and metaphysis were reformatted using 3D software. We measured the epiphyseal tubercle (height, width and length), the metaphyseal fossa (depth, width and length) and the peripheral cupping of the epiphysis. All measurements were normalized to the diameter of the epiphysis. Pearson’s correlation analysis was used to assess the correlations between the variables measured and BMI percentile adjusted for age. Results Following adjustment to age, increased BMI correlated to decreased tubercle height (r =-0.34; 95% confidence interval (CI) -0.53 to -0.11; p = 0.005), decreased tubercle length (r = -0.32; 95%CI -0.52 to -0.09; p = 0.008) and decreased tubercle width (r = -0.3; 95% CI -0.5 to -0.07; p = 0.01). There was no correlation between BMI and metaphyseal fossa and epiphyseal cupping measurements. Conclusion The association between increased BMI percentile and decreased epiphyseal tubercle size, without changes of the metaphyseal fossa and peripheral cupping suggests another morphological change of the femur that may be associated with decreased growth plate resistance to shear stress. Further study is necessary to investigate whether the epiphyseal tubercle size plays a role in the pathogenesis of slipped capital femoral epiphysis in obese children and adolescents. Level of Evidence Level IV