The management of localised and advanced gastrointestinal stromal tumours (GISTs) in terms of histological diagnosis, surgery, imaging, medical treatment and molecular biology has rapidly changed since introduction of imatinib mesylate for molecularly targeted therapy in 2000. In this minireview, we briefly summarise and discuss the current data relevant to the increasing role of molecular characterisation of GISTs in the diagnosis, risk assessment and effective targeted therapy.