Abstract: 　Objective　To explore the clinical phenotype of 22q11.2 deletion syndrome with imperforate anus. Methods　The clinical diagnosis and treatment of one case of 22q11.2 deletion syndrome complicated with anal atresia were retrospectively analyzed. Gene and phenotype of this disease were analyzed, and the related literature was reviewed. Results　An elder male test tube infant of twins, born to a G2P2 mother were found to have special facial features, cleft palate, congenital heart disease, and imperforate anus after birth. A genome-wide microarray scan revealed 22q11.2 deletion syndrome. In related literatures, 22q11.2 deletion syndrome could be affected by TBX1 gene, histone modification, Ranbp1 gene, and even microRNA; while imperforate anus were influenced by multiple elements such as genetic, maternal, and environmental factors and multiple embryonic developments related genes could be involved in its pathogenesis. Conclusions　Congenital imperforate anus and 22q11.2 deletion syndrome are mostly sporadic cases in epidemiology and are incidental accidents in development. Whether there is a common interaction factor between them needs to be further studied and defined.