Expression of the sucrase-isomaltase (SI) gene is induced in cells transitioning from the crypt to the villus of rat jejunum. In the present study, we revealed by ChIP assay using a cryostat sectioning technique that binding of the di-acetylated histone H3 at lysine 9/14 and the transcriptional factor Cdx-2 to the promoter region on the SI gene, as well as mRNA, increased in the transient process. Additionally, di-/tri-methylation of histone H3 at lysine 9/14 on the promoter region of the SI gene rapidly decreased with increasing mRNA. These results suggest that induction of the SI gene during the transition from the crypt to the villi is associated with changes in histone H3 modifications from methylation at lysine 9 to di-acetylation at lysine 9/14, as well as increased binding of Cdx-2 to the SI promoter region.