Postmenopausal women on estrogen replacement therapy (ERT) have a reduced risk of developing colon cancer compared with postmenopausal women not on ERT, suggesting a role for estradiol (E2) in protection against this disease. To determine whether E2 protects against inflammation-associated colon cancer when administered following the initiation of colonic DNA damage, in this study, we implanted E2-containing pellets into mice after co-treatment with azoxymethane and two rounds of dextran sulfate sodium (DSS). Wild-type (WT) E2-treated mice had reduced numbers and average area of adenocarcinomas compared with the control mice. These effects were lost in estrogen receptor-β (Erβ (Esr2)) knockout mice. Surprisingly, apoptosis was reduced and cell proliferation was increased in sections from tumors of the WT E2 mice compared with the WT control mice. These findings are probably due, in part, to a reduction in ERβ expression in colonic epithelial cells as the cells progressed from a non-malignant to a cancerous state as enhanced apoptosis was observed in normal colonocytes expressing higher levels of ERβ. Furthermore, epithelial cells within the tumors had dramatically increased ERα mRNA and protein expression compared with the non-diseased mice. We conclude that while E2 treatment resulted in an overall suppression of colonic adenocarcinoma formation, reduced ERβ expression accompanied by enhanced ERα expression caused an altered colonocyte response to E2 treatment compared with the earlier stages of colon cancer development. These data are the first examples of decreased ERβ expression concurrent with increased ERα expression as a disease develops and highlight the importance of understanding the timing of E2 exposure with regard to the prevention of inflammation-associated colon cancer.