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This is the first reported case of a mesenteric lymphatic malformation in a toddler in Malaysia. It is a rare benign condition with incidence of 1 in 250,000 populations. Our patient presented to us at 2 years 11months old complaining of abdominal distension for 6 months without obstructive symptoms. Clinically there was a vague soft central abdominal mass. CT abdomen done revealed a large multiloculated intraperitoneal mesentery cystic mass within the central abdomen extending to pelvis. A semi-emergency laparotomy was performed. Intra-operatively the multiloculated mesenteric cyst measured 20cm x 30cm, adherent to the small bowel beginning at 12cm from duodeno-jejunal junction. Resection of the mesenteric cyst with adherent small bowel and primary anastomosis was done. Histopathological examination revealed multiple large lymphatic channels of various sizes in the mucosa and submucosa. Our patient has no signs of recurrence and remains symptom-free after 1 year since his surgery. Surgery with clear margins of resection is the recommended gold standard based on available literature. Type of surgical resection required will depend on the type of mesenteric lymphatic malformation. An awareness of this rare pathology is required to ensure proper management is given to these patients.