Advances in the field of GIST accumulate very rapidly. The objective of this short review is to underline their consequences for the diagnostic practice and for the understanding of their pathogenesis. The diagnosis of GIST still relies on histology and immunohistochemistry; this is only in the case of the very rare KIT-negative tumors that other markers (such as DOG-1 and PKCtheta) have to be considered and that the identification of mutations of KIT et PDGRA may have a diagnostic interest. A new prognostic classification of GIST has been proposed: it acknowledges the existence of truly benign GISTs and is adapted to the primary site of the lesion in order to underline the usually better prognosis of gastric GISTs. The search for mutations of KIT et PDGRA must be done in specialized laboratories. It is important for the evaluation of the sensivity to imatinib, and to the other targeted therapies which may find a role in the treatment of advanced tumors, especially of imatinib-resistent GISTs. Much remains to be done in order to decipher the molecular mechanisms responsible for tumor progression in GISTs: their knowledge will be important to validate new prognostic markers.