We isolated cell lysate proteins from PBMCs obtained from 71 children and adolescents (age 5-18) with normal weight, overweight or obesity. Body composition was measured using bioelectrical impedance analysis. Nano-electrospray liquid chromatography-tandem mass spectrometry was used to measure protein abundances. Controlling for patient sex, we investigated changes in abundance depending on leukocyte counts and on percentage body fat (PBF). We show protein expression in PBMCs is altered in children with increased PBF, especially in mitochondrial proteins. These obesity-associated changes in are better explained by PBF than by purely height and weight-based metrics, supporting the utility of bioelectrical impedance analysis in obesity research.