A group of secreted peptides (trefoil factor family; TFF) is abundantly expressed at mucosal surfaces of the gastrointestinal tract and promote epithelial restitution. They are upregulated around areas of epithelial damage, ulceration and neoplasia. The transcriptional regulation of the three human TFF genes was assayed by multiplex RT-PCR and reporter gene analysis in 8 gastrointestinal carcinoma cell lines. The level of endogenous mRNA matched well the reporter gene activity of all TFFs, indicating that the cis-acting elements located less than 1,000 bp upstream of the TATAA box account for cell-specific gene expression. In HT-29, the endogenous TFF expression profile changed in relation to cell growth conditions. Deletion and mutation analysis of TFF promoter constructs revealed enhancing elements shared within the three TFF promoters that were shown to bind nuclear proteins. Thus such specific DNA-protein interaction may explain the TFF peptides' cell specific expression pattern and altered levels in pathological conditions.