The turnaround time for diagnosis of maple syrup urine disease (MSUD) by classic serum amino acid analyses often requires 3-4 days. This is due to the need for branched-chain amino acids (BCAA) to accumulate in the serum of the newborn before testing. The accumulation of BCAAs in infants with MSUD during this time increases the risk of the infant becoming clinically symptomatic. We have developed a noninvasive DNA-based mismatch PCR-RFLP assay for the Y393N BCKDHA allele (E1alpha gene of the branched chain alpha-keto acid dehydrogenase complex), the primary cause of MSUD in Old Order Mennonite communities. The homozygosity and high frequency of this mutation in the Mennonite community and its prevalence in compound heterozygote non-Mennonite MSUD patients is of significance. We describe carrier testing, present the results of nine newborns diagnostically evaluated for the Y393N BCKDHA allele, and demonstrate the efficacy of this PCR-RFLP assay for determining clinical status within 24 h after birth. Analyses within the first 24 h of life allow for immediate diagnosis and treatment of infants homozygous for the Y393N MSUD defect. This is a significant improvement over the time required by current serum amino acid analysis methods.