BACKGROUND: Putative breast cancer stem cells might express surface markers such as aldehyde dehydrogenase 1 (ALDH1) and BMI-1 proteins. The aim of this study was to explore the expression of these proteins in breast cancers from an African population and their associations with the basal-like phenotype (BLP) and other molecular characteristics. METHODS: We analysed 192 paraffin-embedded breast carcinoma samples by tissue microarrays and immunohistochemical methods. RESULTS: In total, 88 tumours (48%) expressed ALDH1, whereas 46 (25%) expressed BMI-1 protein. Expression of ALDH1 was associated with high histological grade (Po0.0005), high mitotic count (Po0.0005), high nuclear grade (Po0.0005), oestrogen receptor (ER) negativity (Po0.0005), progesterone receptor (PR) negativity (P ¼ 0.009), p53 expression (P ¼ 0.034), cytokeratin 5/6 positivity (P ¼ 0.008), epidermal growth factor receptor (EGFR) expression (P ¼ 0.015) and the BLP (Po0.0005), whereas it was inversely associated with BMI-1 staining (P ¼ 0.009). On the other hand, BMI-1 expression was associated with low histological grade (P ¼ 0.004) and ER positivity (P ¼ 0.001). CONCLUSION: There was a high prevalence of ALDH1 expression among breast carcinomas and associations with basal markers and features of aggressive tumours. Studies are required to elucidate the importance of these findings for improved understanding of breast cancer biology.