Thiamine deficiency, a frequent complication of alcoholism, plays an important role in the pathogenesis of the Wernicke-Korsakoff syndrome [WKS]. Previous work by a number of investigators has implicated the thiamine-utilizing enzyme transketolase [Tk] as being involved mechanistically in the genetic predisposition to WKS. In particular, Tk derived from fibroblasts has been found to have an increased Km app for its cofactor thiamine pyrophosphate [TPP] and/or exist in different isoelectric forms in alcoholic patients with WKS as compared with unaffected individuals. We have demonstrated that these differences are not due to different Tk alleles, tissue-specific Tk isozymes, or differential mRNA splicing. These findings point to other mechanisms to explain the biochemical Tk variants, such as differences in assembly of the functional holoenzyme or differences in modification of the primary translation product. Tk assembly or modification, once biochemically characterized, may be found to be subject to genetic variation.