Obesity and its complications are emerging problems in pediatrics. Non-alcoholic fatty liver disease (NAFLD) is increasingly common and indirectly screened for by the level of serum alanine aminotransferase (ALT). We present outcome data on the level of ALT after participation in a comprehensive weight management program for overweight children and adolescents. A retrospective chart review was performed on patients enrolled in the NEW (Nutrition, Exercise, Weight Management) Kids Program at the Children's Hospital of Wisconsin from June 2003 to November 2005. Ninety days of participation and ALT > 35 IU/L were required for inclusion. Demographic, anthropometric, and laboratory parameters for the population were recorded. Twenty-two cases fulfilled inclusion criteria. Population was 67% male and had an age of 10.1 + 2.9 (mean + SD) years; range 4.8-17.2. Medications included standard multivitamin doses. After 271 + 145 (mean + SD) days in the program, there was a decrease in BMI z-score and serum ALT that occurred without change in fasting lipids, insulin or glucose. Participation in a lifestyle modification program results in decreased body mass and serum ALT. These data suggest that small reductions in body mass may result in biochemical improvements and ultimately in a decreased risk for NAFLD without easily discernable improvements in lipemia or insulin resistance.