The native promoter of beta 1,3 galactosyltransferase beta 3Gal-T5 contributes to the expression of the enzyme and its oligosaccharide products, such as Lewis antigens, in many tissues. It is mainly sensitive to nuclear factor NF-Y and located nearby two CpG islands. To elucidate the regulation of the native promoter, we analyzed NF-Y protein and beta 3Gal-T5 mRNA, and found that NF-Y is scarcely modulated among various cell lines and biopsies from normal or cancerous colon. Conversely, beta 3Gal-T5 expression levels vary in the cell lines and are strongly down-regulated in colon cancer. We also performed quantitative methylation analysis of beta 3Gal-T5 CpG islands and found an inverse correlation between mRNA expression and DNA methylation. In particular, the methylation levels of both islands are always increased in cancer, with respect to the corresponding normal counterpart, in matched normal and tumor samples of colon and breast origin. Moreover, treatment with chromatin remodeling agents 5-aza-2\'deoxycytidine and trichostatin A does not restore transcription in completely negative cells, but only increases expression in basally positive cells. However, methylation analysis after 5-aza-2\'deoxycytidine treatment revealed partial demethylation of both islands in all treated cells. Finally, chromatin immunoprecipitation assays on beta 3Gal-T5 promoter showed that histone H3K4 trymethylation, H3K79 dimethylation, and H3K9-14 acetylation are high in cells expressing the transcript, and very low in those negative, while H4K20 trimethylation and H3K27 dimethylation are the opposite. We conclude that complex epigenetic modulation underlies the regulation of beta 3Gal-T5 native promoter.