Chondroid tumours comprise a heterogeneous group of lesions with diverse morphological features and clinical behaviour. Over the past decade, a substantial number of chondroid tumours have been shown to harbour specific genetic abnormalities. These genetic alterations can be divided into two groups: tumours with specific translocations, and tumours with specific gene mutations. These genetic events give not only important insight in the tumourigenesis of chondroid tumours but offers new possibilities for molecular diagnosis. Some of these specific genetic changes have been implemented in routine pathology. This review aims to highlight the molecular genetics of chondroid tumours and their diagnostic applications.