Gastrointestinal stromal tumours (GISTs) are uncommon mesenchymal tumours that originate from the interstitial cells of Cajal. As these tumours are difficult to distinguish from gastrointestinal smooth muscle tumours using standard histological techniques, their true prevalence may be underestimated. Metabolic and systemic consequences of GISTs are not well described in any species. More rarely, neoplasms with histological and immunohistochemical features similar to GISTs may occur outside the gastrointestinal tract, the so-called extragastrointestinal stromal tumours (EGIST). EGISTs have never been described in the veterinary literature. In this article the authors present and describe clinical findings, management and treatment of two dogs with clinical hypoglycaemia induced by histologically confirmed GIST and EGIST. Hypoglycaemia resolved immediately and long term after tumour excision. To the authors’ knowledge this is the first report of hypoglycaemia associated with a canine GIST and the first case report of an EGIST in a dog.