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The association of situs inversus totalis (SIT) and VACTERL syndrome an extremely rare coincidence.The patient was first diagnosed as simple SIT with lumbosacral neoplasms according to the prenatal magnetic resonance imaging (MRI) examination; however, the local hospital ignored the important to physical examination so that missed anal atresia with fistula. The patient was presented to our hospital owing to constipation for 1 week. And then, she was diagnosed as VACTER syndrome with situs inversus totalis.Anorectoplasty was performed to treat constipation, one month later, we performed intramedullary tumor resection and pathological diagnosis of ependymal cyst. Postoperative recovery was uneventful and the baby was doing well at 5-months follow up.It is extremely necessary for careful physical examination and detailed auxiliary examination to each system (including echocardiography, MRI, and so on) when diagnosing SIT. Also, recognizing and understanding the spectrum of situs anomalies is important, which aids in the diagnosis of disease and accordingly plan the therapeutic interventions.