Childhood obesity is associated with a pro-atherogenic phenotype contributing to increased cardiovascular disease (CVD) risk. This single-arm pilot study examined the effects of a lifestyle intervention on lipoprotein particle size and cholesterol distribution in obese Latino adolescents. Fifteen obese Latino adolescents (15.0±1.0 years) completed a 12-week nutrition education and exercise intervention. LDL particle size and distribution of cholesterol in lipoprotein subclasses were determined via polyacrylamide gel electrophoresis. The intervention resulted in increases in mean LDL-particle size (269.3±3.4 to 271.6±2.9Å, p=0.0003) and cholesterol in large HDL subfractions (22.4±11.2 to 26.8±10.6% area, p=0.007) along with decreases of cholesterol in small LDL (1.6±2.0 to 0.6±1.2% area, p<0.01) and HDL subfractions (23.2±9.4 to 19.0±6.7% area, p=0.05). These improvements were observed independent of changes in weight (90.7±26.2 to 89.9±27.8 kg, p>0.05) and suggest that lifestyle modification in obese youth may reduce cardiovascular risk by shifting lipoprotein particle size and cholesterol distribution to a less atherogenic phenotype.