Gender differences in the incidence and behaviour of colon cancer suggest a hormonal influence and epidemiological data suggest a protective effect for hormone replacement therapy. Recently, it has been shown that oestrogen receptor (ER) beta is the predominant ER in colon tissue. The aim of this study was to examine the expression and distribution of ERbeta in normal and colorectal cancer samples, using immunohistochemistry and (in a subset of patients) real-time quantitative reverse transcriptase polymerase chain reaction in a well-defined patient cohort and to correlate this with clinico-pathological outcome. Immunohistochemical analyses of normal colon revealed strong specific nuclear immuno-reactivity in all epithelial cells lining the colonic crypts. In colon cancer, ERbeta expression was lost in 21% of samples irrespective of patient age or gender. Interestingly loss of ERbeta expression was higher in left colon and rectal cancers (27%) compared to right colon cancers (8%). A correlation between loss of ERbeta expression and advanced Dukes stage was observed. Loss of ERbeta with increased Dukes' stage suggests that it may be affording a protective effect against colon carcinogenesis. Its presence may be a favourable prognostic marker in this disease and could explain the protective effect of oestrogens against colon cancer development.