Breast tumours consist of phenotypically diverse populations of breast cancer cells of which only a minority has the ability to form new tumours. The capacity for breast tumour development has been shown to be restricted to breast cancer stem cells with the CD44+/CD24(-/low) phenotype. These cells can resist apoptosis through mechanisms such as the regulation of Bcl-2. Identification of this population of cells is important because of its implication in the development of new therapeutic strategies. One hundred and forty-six primary operable breast cancer patients were investigated in order to identify the population of CD44+ and Bcl-2+ cells in paraffin-embedded tissues by immunohistochemistry. The prevalence of these phenotypes was then correlated with clinicopathological features. CD44 and Bcl-2 expression was detected in 86% and 82% of breast tumours, respectively. There was no significant correlation between CD44+ tumour cell prevalence and tumour characteristics, whereas the prevalence of CD44+ cells was associated with higher levels of Bcl-2 expression (P = 0.004). In univariate analysis, Bcl-2 expression was correlated with breast tumours of lower grade (P < 0.001) and fewer lymphatic metastases (P < 0.05). Our findings suggest that the prevalence of CD44+ tumour cells as a subpopulation of breast cancer stem cells was of no clinicopathological significance, but was correlated with higher Bcl-2 expression. This population of tumour cells may thus be more resistant to apoptosis. Targeting these cells in combination with current treatments may be more effective in treating breast cancer patients.