Recurrent aphthous stomatitis is a disease of unknown cause. To examine whether thiamine (vitamin B1) deficiency is associated with recurrent aphthous stomatitis, we studied vitamin B1 levels in 70 patients with recurrent aphthous stomatitis and in 50 members of a control group. The vitamin B1 level was determined as thiamine pyrophosphate effect on transketolase activity in red blood cell lysates. Low levels of vitamin B1 were detected in 49 patients but in only two members of the control group (p < 0.0001). These low levels were not associated with patient age, sex, or underlying disease causing recurrent aphthous stomatitis. Our finding suggests an association between thiamine deficiency and recurrent aphthous stomatitis.