mRNA expression profiling has been used to define molecular subtypes of human breast cancer. Also microRNAs have been investigated in these breast cancer subtypes. However, little is known regarding the microRNA signature of healthy luminal and basal breast epithelial cells. Therefore, a method is described to isolate immunostained luminal and basal breast epithelial cells in formalin-fixed paraffin-embedded tissues by laser microdissection. Employing this new methodological approach, we could identify distinct microRNA profiles of luminal and basal breast epithelial cells by real-time PCR-based profiling.