Clinical features associated with the deletion of 22q11.2 are highly variable. Most are diagnosed by cardinal congenital heart disease or hypoparathyroidism. In cases without major features, an early accurate diagnosis of 22q11.2 deletion syndrome is difficult. Congenital anorectal malformations (ARM), which can be detected soon after birth, have been rarely reported in 22q11.2 deletion syndrome. We report two cases of 22q11.2 deletion syndrome with ARM who showed growth retardation. ARM was detected in both patients without congenital heart disease or hypoparathyroidism at early infancy and they were followed by pediatric surgeons. Later, failure to thrive or short stature became evident, and they consulted with pediatric endocrinologists who subsequently confirmed the diagnosis of 22q11.2 deletion by fluorescent in situ hybridization analysis. The combination of ARM and growth retardation may lead to an early diagnosis of 22q11.2 deletion syndrome.