Gastrointestinal stromal tumors are the most common mesenchymal tumors of the gastrointestinal tract. The introduction of a number of small molecule tyrosine kinase inhibitors has revolutionized the management of metastatic disease. Surgery is the mainstay of management for localized disease. Patients with high risk tumors are treated with adjuvant imatinib. We report the rare presentation of a localized primary small bowel gastrointestinal stromal tumor in association with multiple liver abscesses. Cystic liver lesions should be fully evaluated in gastro intestinal tumor patients to exclude an infective cause. Treatment with intravenous antibiotics resulted in clinical and radiological improvement of the liver abscesses. The small bowel tumor was treated with surgical resection.