Gastrointestinal stromal tumours (GISTs) are the most common mesenchymal neoplasm of the gastrointestinal tract, while osseous metaplasia of this tumour is an unexpected event. To date, no cases have been reported in the literature. Herein, we report a case of a 60-year-old man affected by a GIST with benign osseous metaplasia and mature bone formation. We also discuss the pathogenesis of intratumoural ossification and review the relevant literature. The prognostic significance of ossification in GIST remains unclear because of the limited cases reported.