Primary malignant fibrous histiocytoma of the gastrointestinal tract is extremely rare. To date, only 10 cases of primary malignant fibrous histiocytoma arising in the small intestine have been reported in the English literature. We describe here the genetic alterations and morphologic features of a primary malignant fibrous histiocytoma arising in the jejunum. Immunohistochemically, the tumor cells expressed vimentin, CD68 and alpha-1-antitrypsin, but were negative for other markers. Ultrastructurally, they showed features of fibroblasts and histiocytes. Immunohistochemical overexpression of p53 and MDM2 was observed. Mutation analysis of the p53 gene detected a missense mutation in codon 158 of exon 5. Our results suggest that p53 gene mutations and MDM2 overexpression may play an important role in the tumorigenesis. To our knowledge, the present report is the first genetic study of this rare lesion.