Objective: To study the relationship of sister chromatid exchange, micronucleus rate, and chromosome structural aberration rate of lymphocytes in recurrent apthous ulcer patients. Methods: Sister chromatid exchange, micronucleus rate, and chromosome structural aberration of 60 recurrent apthous ulcer patients were determined, and were analyzed by noncondition logistic regression. The risk ratio of the 3 study factors was calculated. Results: Sister chromatid exchange, micronucleus rate, and chromosome structural aberration were important risk factors among the many complicated causes of recurrent apthous ulcer. Conclusion: The results of the study essentially showed that recurrent apthous ulcer patients could have some pathological genetic predisposition and abnormal genetic material.