Background: Colonic transformation is thought to be a phenotypic alteration in the ileum after total colectomy (TC) but has not been well addressed at the molecular level. We previously demonstrated roles of aldosterone in enhancement of ileal sodium absorption after TC. However, the significance of aldosterone in intestinal adaptation has been unknown. Methods: Rat epithelial gene expression was compared between the ileum and distal colon by complementary DNA microarray. Genes were categorized into "colonic," "common," and "ileal" genes according to signal intensity. Ileal gene expressions in (1) the control and TC rats and (2) the control and aldosterone-infused rats were compared to detect altered genes or to assess the role of aldosterone in intestinal adaptation. Differential expression of MUC3 and lysozyme was confirmed by quantitative reverse transcriptase-polymerase chain reaction. Results: A total of 6109 genes were categorized into "colonic," "common," or "ileal" gene pools. A comparison of the control and TC rats yielded 82 and 91 genes that were induced and suppressed in the ileum after TC, respectively. Thirty-five percent of them were associated with colonlike transformation (ie, the induction of colonic genes or the suppression of ileal genes). The expressions of MUC3 and lysozyme messenger RNAs were enhanced significantly in the TC ileum, compared with the control. In comparison, aldosterone infusion modulated a total of only 21 genes in the ileum. Conclusion: Those data demonstrate that altered gene expression after TC is, in part, characterized by colonlike transformation. Furthermore, circulating aldosterone appears to play a part in the altering and/or adapting of gene expression in intestinal epithelium.