Gastointestinal stromal tumours (GIST) are the most common mesenchymal neoplasms of the digestive tract. They originate from the interstitial cells of Cajal. GIST are not regarded as benign tumours, and morphological risk assessment is generally recommended according to the NIH consensus adapted from Fletcher et al. Other classifications (Miettinen and Lasota, Joensuu) considering the tumour site and tumour integrity as individual criterion may give different assessment results. Therefore, a special note has to be given in a proper histopathological diagnosis, referring to the system of risk assessment used. The histological diagnosis of GIST requires immunohistochemistry (CD117, PDGFRalpha). In doing so the use of a panel of antibodies is recommended helpful to cover all differential diagnostic relevant possibilities of mesenchymal neoplasms of the digestive tract. Analysis of the hot spot regions of KIT and PDGFRalpha genes is important for therapy planning and also may have some prognostic significance, for which reason it is recommended to be performed in GIST regularly.