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Abstract Background The diagnosis of obscure gastrointestinal bleeding (OGIB) which is defined as bleeding of unknown origin of the small bowel by routine evaluation in childhood is a challenge. Case presentation Here we report a one-year-old Chinese girl who was suspected with idiopathic pulmonary haemosiderosis (IPH) and referred to our department for further diagnosis. Finally she was diagnosed with vascular malformations (VM) by exploratory laparoscopy combined with pathological examination. Conclusions Children OGIB could be easily misdiagnosed in the beginning, and OGIB children with active ongoing bleeding may benefit from proceeding directly to exploratory laparoscopy, followed by pathological confirmation of the diagnosis.