To analyse the phenotype of breast tumours that express oestrogen receptor-b (ERb) alone tissue microarrays were used to investigate if ERb isoforms are associated with specific prognostic markers and gene expression phenotypes in ERa-negative tumours. ERa-negative tumours were positive for ERb1 in 58% of cases (n ¼ 122/210), total ERb in 60% (n ¼ 115/192) and ERb2/cx in 57% of cases (n ¼ 114/199). Oestrogen receptor-b1 and total ERb were significantly correlated with Ki67 (r ¼ 0.28, Po0.0001, n ¼ 209; r ¼ 0.29, Po0.0001, n ¼ 191) and with CK5/6, a marker of the basal phenotype (r ¼ 0.20, P ¼ 0.0106, n ¼ 170; r ¼ 0.18, P ¼ 0.0223, n ¼ 158). ERb2/cx was strongly associated with p-c-Jun and NF-kBp65 (r ¼ 0.53, Po0.0001, n ¼ 93; r ¼ 0.35, Po0.0001, n ¼ 176). This study shows that a range of ERb isoform expression occurs in ERa-negative breast tumours. While expression of ERb1, total and ERb2/cx are correlated, individual forms show associations with certain phenotypes that suggest different roles in subsets of ERanegative cancers. Based on our in vivo observations, ERb may have the potential to become a therapeutic target in the specific subcohort of ERa-negative breast cancers.