Two techniques were used to seek variants of human erythrocyte transketolase and to test for any association of the Wernicke-Korsakoff syndrome, a thiamin-deficiency disease, with a particular variant of this thiamin-dependent enzyme. Apparent Km values for the cofactor thiamin diphosphate were similar for patients and controls. However, isoelectric focussing separated erythrocyte transketolase into different isoenzymes characterized by pI values in the range 6.6-9.2. Six distinct patterns of isoenzymes were found in thirty-six healthy control subjects. The isoenzyme pattern for thirty-nine out of forty-two patients suffering from the Wernicke-Korsakoff syndrome was identical to a pattern found in only eight of thirty-six control subjects, a highly significant association (P less than 0.001). This association suggests that a variant transketolase and thiamin deficiency together contribute to the pathogenesis of the brain damage of the Wernicke-Korsakoff syndrome by some mechanism independent of apparent Km values for thiamin diphosphate.