Anorectal malformation: This is the most common cause of imperforate anus, resulting from abnormal development of the rectum and anus during embryogenesis. It can range from mild anomalies to complex cloacal malformations.

Hirschsprung's disease: Although primarily characterized by congenital aganglionosis of the colon, it can sometimes present with imperforate anus due to associated anorectal malformations.
Cloacal exstrophy: A rare congenital anomaly involving the abdominal wall, genitourinary, and gastrointestinal systems, which can include imperforate anus as part of its spectrum.
VACTERL association: A non-random association of birth defects including vertebral anomalies, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities, where imperforate anus is a key feature.

Spinal dysraphism: Conditions like spina bifida can be associated with anorectal malformations and imperforate anus. Missing this diagnosis could lead to neurological complications.
Genitourinary anomalies: Many cases of imperforate anus have associated genitourinary anomalies, which, if not identified and managed, could lead to significant morbidity.

Caudal regression syndrome: A rare condition often associated with maternal diabetes, characterized by abnormal development of the lower spine, which can include imperforate anus.
Sirenomelia: A very rare congenital anomaly characterized by fusion of the lower limbs, often associated with other severe malformations including imperforate anus.
Congenital megacolon: Though more commonly associated with Hirschsprung's disease, it can rarely present with or lead to complications resembling imperforate anus in the neonatal period.