To investigate effects of maternal diabetes and metformin treatment on metabolic newborn screening (NBS) results of infants born to mothers with hyperglycemia during pregnancy. Retrospective case-control study. NBS results of infants born to mothers treated with metformin for hyperglycemia during pregnancy were compared with diet-treated subjects with diabetes and matched normal control subjects. maternal type 1 diabetes, major fetal anomalies, and incomplete infant data. Inclusions: maternal hyperglycemia in pregnancy treated with diet alone or diet plus metformin. Results from the New South Wales Newborn Screening Program (dried infant blood spot sample, 24-72 h after birth) for 25 routinely studied analytes were measured using mass spectrometry. Data from metformin-exposed and control infants were compared using nonparametric methods and multiples of the median for each analyte. A total of 574 case subjects were compared with 952 diet-treated case subjects with diabetes and 979 control subjects. Metformin-exposed infants had shorter gestational age (266 ± 7 vs. 272 ± 10 vs. 274 ± 9 days) (P < 0.001) and lower birth weights (3.28 ± 0.51 vs. 3.29 ± 0.49 vs. 3.33 ± 0.43 kg) (P = 0.008). Short-, medium-, and one long-chain acylcarntine (tetradecanoylcarnitine [C14]) concentrations were higher in the metformin-exposed group compared with normal control subjects. Comparison with diet-treated control subjects with diabetes (to eliminate confounding by hyperglycemia) continued to show raised butyrylcarnitine (C4), isovalerylcarnitine (C5), and glutarylcarnitine (C5D) in the metformin-exposed group. There was no evidence of vitamin B12 deficiency (low methionine and elevated propionylcarnitine [C3]) in metformin-exposed infants. All results were within normal population limits. We have identified subtle (nonpathological) changes in neonatal metabolism that represent a signature effect of fetal metformin exposure.