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Agenesis of the dorsal pancreas is a rare congenital anomaly caused by underdevelopment or agenesis of the dorsal pancreatic bud that forms the upper head, neck, body and tail of the pancreas. We report a case of agenesis of the dorsal pancreas, which was found under examination of diabetes mellitus (DM). A 16-year-old girl was transferred to our hospital because of a positive urine glucose reading during a school-conducted examination. Abdominal computed tomography and magnetic resonance cholangiopancreatography revealed the deficit of the pancreatic body and tail. Diabetes-associated autoimmune antibodies were negative in a blood test. Decreased beta-cell function was demonstrated by oral glucose tolerance and glucagon stimulation tests. Although the notion that agenesis of the dorsal pancreas leads to decreased endocrine or exocrine function is controversial, the results of this study suggest that we should consider these causes of diabetes mellitus. When treating a young patient with diabetes mellitus, we should consider causes of diabetes mellitus such as congenital anomaly or maturity onset diabetes, in addition to type 1 and type 2 diabetes mellitus.