Gastrointestinal stromal tumours (GISTs) are mesenchymal tumours that can be located in any part of the gastrointestinal system. Most often they occur in the stomach and in 20-30% of cases they occur in the small intestine. About 30% of all GISTs are malignant. We report a case of a 54-year-old patient with malignant GIST located in the small intestine and liver. The patient complained of discomfort and heaviness in the abdomen and parts of the abdomen were hard on palpation. Family physician performed an ultrasound of the abdomen which showed a large mass in the right hemiabdomen. CT scan of the abdomen showed a tumour mass of approximately 13x19x20 cm and GIST was suspected. Biopsy was performed and histopathological finding spoke in favour of GIST. GIST resection and Meckel diverticulum resection were performed. Histopathological finding confirmed it was a malignant GIST. After nine months, a control ultrasound showed an oval formation of the liver and excision was performed. The patient was discharged home and histopathological finding confirmed that liver formations were also GIST. GIST should be considered as a possible cause of abdominal difficulties and the treatment of choice is surgery.