Gastrointestinal stromal tumours (GIST) represent a heterogeneous group whose classification frequently requires ultrastructural and immunohistochemical studies. In a retrospective study of the ultrastructural findings of 24 gastrointestinal stromal tumours, whose light microscopic study has yielded ambiguous results and in which accurate diagnosis had required ultrastructural support, seven were found to have the characteristics of gastrointestinal autonomic nerve (GAN) tumours. In all of them the diagnosis was based on the presence of dendritic processes with dense neuroendocrine granules. Immunohistochemically, the seven tumours were negative for smooth-muscle markers. All stained positively for vimentin. NSE, chromogranin, and synaptophysin were positive in most of them, while S-100 protein was positive only in two cases. We present the ultrastructural and immunohistochemical features of seven GANT against the background of the GISTs of our series. We conclude that GAN tumours cannot be diagnosed by light microscopy alone but this tumour group displays characteristic electron microscopic and immunohistochemical features and appears to represent a distinct type of GIST.