Gastrointestinal stromal tumour (GIST) is now recognised as the most common primary mesenchymal tumour of the gut. A number of different parameters have been identified to aid prediction of clinical behaviour, but prognostication for an individual remains difficult. The pathologist plays a crucial role in guiding management of these tumours, but is faced with a number of challenges in so doing. This review describes the variable pathological features that may be encountered, and examines some of the issues in the pathology reporting of GIST and attempts to provide some guidance in factors that should be addressed in a comprehensive pathology report. © 2013 Royal College of Pathologists of Australasia.