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Abstract Background Intussusception with intestinal malrotation is termed as Waugh’s syndrome. The incidence of Waugh’s syndrome is less than 1%. There are very few reported cases. Once presented, it is a pediatric surgical emergency. Case presentation We present here two cases of Waugh’s syndrome: an 11-month-old male patient of Punjabi descent and a 4-month-old female patient of Afghan descent who presented to us with abdominal pain and bleeding per rectum. Abdominal sonography revealed an intussusception with a target sign. They were explored and perioperatively had intestinal malrotation alongside intussusception, thus a diagnosis of Waugh’s syndrome was made. A right hemicolectomy and Ladd’s procedure was performed. Conclusion Waugh syndrome is a rare congenital anomaly but can present with vague abdominal symptoms. Once presented, it is a pediatric surgical emergency. The patient should be optimized followed by surgical exploration.