Hereditary multiple intestinal atresia (HMIA) is a rare form of intestinal atresia that affects the gastrointestinal tract from the pylorus to the rectum. A few cases have been reported in the literature. Here, we report the case of a three-day-old girl who was referred to our hospital as a case of upper intestinal obstruction. After initial resuscitation, the radiological examination revealed pyloric obstruction, multiple intra-abdominal calcifications, and rectal atresia making the diagnosis of HMIA most likely. Exploratory laparotomy revealed multiple intestinal atresia, the first started at the pylorus, the second was at the level of the duodenojejunal junction, and there were also multiple small bowel atresias. The colon was a cord-like structure, and there was rectal atresia. Multiple resections of the atretic intestinal segment followed by multiple anastomoses, terminal ileostomy, and the use of a trans-anastomotic tube were performed. In this study, the clinical picture, radiological findings, and management are described and compared to the findings reported in the literature.