Recurrent aphthous ulcer (RAU) is the most common ulcerative disease of the oral mucosa. Although RAU appears in all ages, the onset of RAU peaks during childhood. Childhood RAU, as a special patient group, displays distinct etiology. The etiology of childhood RAU includes genetic, local trauma, psychologic, nutritional factors, microbial infection, and abnormal immunologic response. Moreover, some cases of childhood RAU are associated with several systemic diseases. This article presents the current progress on the etiology of RAU in children.