Gastrointestinal stromal tumours (GISTs) are fairly rare neoplasms, constituting less than 3 % of all gastrointestinal malignancies. The integration of molecularly targeted treatment regimes (i.e., tyrosine kinase inhibitors) in clinical oncology has revolutionized the management of patients with irresectable GISTs or metastatic disease. Malignant GISTs usually display increased glucose metabolism and therefore 18F-fluorodeoxyglucose (FDG) uptake within the scope of positron emission tomography (PET) scans. Nowadays, dual-modality FDG PET/CT (computed tomography) imaging is of considerable value in diagnostic work-up of patients with GISTs acquiring functional and anatomic information simultaneously. The following article sheds light on the impact of FDG PET and combined FDG PET/CT imaging in initial disease evaluation, detection of tumour recurrence and the early assessment of treatment response to molecularly targeted agents such as imatinib mesylate or sunitinib maleate.