Background: To determine the effects of metformin therapy in children with metabolic syndrome (MS). Methods: A retrospective electronic chart review in children aged 8-18 years, from 2000 to 2012 with a diagnosis code for MS (ICD 277.7) that met the modified NCEP ATPIII criteria for MS. Results: There were a total of 217 subjects, 150 in the non-metformin [untreated group (UTG)] and 67 in the metformin treated group (MTG). At baseline, the MTG had a body mass index (BMI) similar to UTG, but had higher total cholesterol, low-density lipoprotein cholesterol (LDL-C), and non-high density lipoprotein cholesterol (non-HDL-C). At the end of 1 year, the MTG (n=28) had reduced weight percentile (99.4±0.7 vs. 98.9±1.7, p=0.03), BMI percentile (99.2±0.5 vs. 98.8±1.1, p=0.012), total cholesterol (194.9±45.8 vs. 177.9±32.5 mg/dL, p=0.04), LDL-C (128.3±44.7 vs. 113.8±36.0 mg/dL, p=0.04), and non-HDL-C (154.6±45.5 vs. 136.4±35.2 mg/dL, p=0.03) compared to their baseline. The UTG (n=56) did not have any significant change in those parameters. Conclusions: Metformin treatment results in significant improvement in BMI, total cholesterol, LDL-C, and non-HDL-C in children with MS.