A case of gastrointestinal autonomic nerve tumour with light microscopic, immunohistochemical and ultrastructural examination is reported. The tumour was composed of spindle cells or large cells with clear cytoplasm and showed intense staining for vimentin and focal staining for neuron-specific enolase, chromogranin, synaptophysin, gastrin, P substance and S-100 protein. Ultrastructural examination showed long processes with dense core granules and the absence of features characteristic of other gastrointestinal stromal tumours. In addition we noted small traces of basal lamina and the absence of synaptic vesicles. It seems that the biological behaviour of gastrointestinal autonomic nerve tumours is aggressive but there are too few reports on which to conclude anything about their prognosis. Our findings suggest that tumour has a neuroectodermal differentiation.