Medium chain acyl-CoA dehydrogenase deficiency (MCAD) is a defect in the mitochondrial oxidation of fatty acids. The disorder typically presents with episodes of vomiting and hypoglycemia, sometimes with changes in mental status and hepatic failure. These Reye's-like features may culminate in coma and death. Stress, intercurrent illness, and reaction to childhood immunization have been shown to precipitate acute metabolic episodes in MCAD patients. All cases are caused by mutations of the single MCAD gene on chromosome 1. Most clinically ascertained cases are caused by an A985G transition in exon 11. Here we report the preliminary findings of MCAD patients detected prospectively through a supplemental newborn screening program in Pennsylvania using tandem mass spectrometry. From the first 80,371 newborns screened we prospectively found nine babies with MCAD (1/8930) plus two additional newborns screened because of a previously known family history. Molecular analysis showed 56% of the detected patients to be compound heterozygotes for the A985G and a second mutation. This is in contrast to clinical retrospective studies which have found only 20% to be compound heterozygotes. We have identified two of the other mutations including a novel mutation (DG91/C92, 6-bp deletion) in one of our patients by using single-stranded conformation polymorphism (SSCP) and sequence analysis of conformers. Our results confirm that MCAD is one of the more common inborn errors of metabolism. The different mutation frequencies observed between retrospective clinical studies and our prospective newborn screening study suggest that clinical ascertainment may lead to preferential identification of the A985G mutation.