Introduction Cystic lesions involving the gastrointestinal tract are rare in infants and children. Clinical presentations include asymptomatic lesions, pain abdomen, mass per abdomen and vomiting. The aim of the present study is to study the acute presentation of cystic lesions of the gastrointestinal tract in pediatric patients. Methods All patients below the age of 12 years with acute abdomen in the setting of a gastrointestinal cyst were included in the study. The patients underwent ultrasound of the abdomen or CECT or both. All patients underwent laparotomy. Either resection and anastomosis or excision of cyst was done for all patients. Results 16 patients were included in the study. The age of the patients ranged from 1 day to 12 years. The most common presenting symptoms were abdominal pain, distension and vomiting. Most common signs were abdominal lump, distension and tenderness. Ultrasound was done in 14 cases, CECT was done in 10 patients. Resection and end to end anastomosis was done in 11 cases and excision of the cyst was done in 5 cases. Conclusion Cystic lesions of the gastrointestinal tract can present in children of both sexes at any age. Due to the improvement in antenatal scans some of these cystic lesions can be diagnosed antenatally. Nearly two thirds of the cystic lesions of the abdomen present with an acute abdomen. All these patients require immediate surgical management. The cysts which are in proximity with the bowel are more prone for complications. The management may involve resection and anastomosis of involved or excision of cyst.