Rationale: Duodenal atresia in association with situs inversus abdominus is extremely rare. Care should be taken when selecting appropriate surgical methods, and caution should be exercised during the surgery to avoid misdiagnosis and mistreatment. With prompt recognition of the condition, the surgical procedure should be performed in a timely manner to achieve positive results. Patient concerns: A newborn affected by situs inversus abdominus associated with duodenal atresia, midgut malrotation, and volvulus. Diagnosis: Congenital duodenal atresia with situs inversus abdominis. Interventions: Diamond-shaped duodenoduodenostomy with appendectomy was performed, with the release of Ladd band and correction of the malrotation. Outcomes: The baby boy is thriving well with no abdominal complaints at 4 years of surgical follow-up. Lessons: Although several theories are put forward to clarify this matter, the proper cause of duodenal atresia is not well defined. Clinical symptoms and examinations can assist diagnosis, the definitive cause should be ascertained by surgical approach. And the operating surgeon must be aware of the “mirror anatomy” to prevent unnecessary injuries. Additionally, long-term prognosis for duodenal atresia are very good, therefore, careful attention in postoperative management are important in such a case.