Hypospadias is a congenital anomaly of the external genitalia of the male animals. 30 days old German shepherd pup was reported with difficulty in defecation and urination. Radiography of abdomen revealed megacolon with impacted faeces. At necropsy hypospadias, an improper fusion of the distal urethra and a small penis without the prepuce cover and urethra opening located ventral to anus, atresia ani with a small urethro-rectal fistula and megacolon dilated five times the normal size up to a length of 19 cm, with impacted faeces were observed. Based on the history, clinical signs and necropsy lesions the pup was confirmed as hypospadias complicated with megacolon. To our best of knowledge, this is the first report of hypospadias complicated with megacolon in a pup.