Esophageal atresia, is a congenital anomaly that is seen in 1 of 2500 births and can be treated surgically. Patients can be fed orally after the anomaly is surgically corrected. Especially surgical complications should be ruled out in cases where the patient's general condition becomes worse after being fed. If the patient's general health condition still persists, then metabolical disorders should be considered. Methylmalonic acidemia was detected in further investigations of a newborn who was operated for isolated esophageal atresia in our clinics, and developed metabolical acidosis after being fed postoperatively. Although prognosis is good after early diagnosis and treatment of organic acidemias as methylmalonic acidemia, the diagnosis might be delayed as it is a rare condition that does not firstly come to mind, and in these patients permanent disabilities might develop. As our literature review revealed our case report is the first case in the literature, since concomitancy between esophageal atresia and organic acidemias has not been reported in the literature.