Oesophageal gastrointestinal stromal tumours (GISTs) are rare in comparison to those of the stomach and intestines. Recently, it has been clarified that mutations of the c-kit gene resulting in gain of function might be associated with histogenesis of this type of tumour arising in the stomach and intestines. We describe an oesophageal GIST on immunohistochemical and genetic analyses of the gene. A 71-year-old man had an intramural tumour of the middle third of the oesophagus. Tumour cells were composed predominantly of spindle-shaped and partially epithelioid cells. They were diffusely positive for CD117. Six base deletion resulting in in-frame mutation of the c-kit gene was confirmed at codon 556-558 (cag tgg aag to cag) of exon 11. Patients with mutations of the c-kit gene revealed worse prognoses in GISTs arising from other locations. A long-term follow-up observation is needed for the case.