Breast cancer can be classified into several subtypes based on gene expression profiling. Basal‐like breast carcinoma (BLC) has a triple negative phenotype, that is, the subtype lacks the estrogen receptor (ER), progesterone receptor (PgR) and human epidermal growth factor receptor 2 (HER2). It has been recently reported that CD109, a glycosylphosphatidylinositol (GPI)‐anchored cell surface protein, is a new breast myoepithelial marker. In the present study CD109 expression was investigated in invasive ductal carcinomas (IDC) of the breast on immunohistochemistry. Eighty‐eight formalin‐fixed, paraffin‐embedded breast carcinoma sections were immunostained with anti‐CD109, anti‐cytokeratin 5/6 (CK5/6), anti‐calponin, anti‐vimentin and anti‐p63 antibodies. CD109 expression was detected in 18 of 30 basal‐like breast carcinomas (BLC) but not in other types of 53 IDC (non‐BLC) that were positive for ER, PgR and/or HER2. The percentage of CD109‐positive tissues (60%) in BLC was similar to that of CK5/6 (63%) and higher than that of other myoepithelial markers including p63 (23%), calponin (33%) and vimentin (33%). Statistical analysis indicated that the CD109‐positive group in BLC, but not the CK5/6‐positive group in BLC, was associated with reduced fat invasion (P < 0.05). These findings indicate that CD109 is a useful diagnostic marker for BLC and that CD109 expression may affect biological properties of cancer cells.