Some patients with maple syrup urine disease respond to thiamine administration with a reduction in ketoaciduria and increase in activity of branched-chain alpha-ketoacid dehydrogenase. The biochemical mechanism underlying this effect is unknown but may result from decreased affinity of the mutant enzyme for thiamine or from stabilization of the abnormal enzyme by thiamine. The E1 alpha subunit of the complex participates in the thiamine-dependent decarboxylation of branched-chain alpha-ketoacids. We sequenced the E1 alpha subunit by using reverse transcription of RNA followed by enzymatic amplification of cDNA in two patients with thiamine-responsive maple syrup urine disease. The deduced amino acid sequence of this subunit in the patients was identical to that in normal controls, suggesting that in the patients the thiamine-binding site is abnormal because of a mutation in the E1 beta subunit. Other possible explanations are (a) that a mutation in the E1 beta or E2 subunits either alters thiamine binding by E1 alpha because of allosteric interactions or causes the complex to be unstable and (b) that thiamine stabilizes the complex.