MicroRNAs are likely to play pivotal roles in both stem cells and cancer, and are further promising candidates for future therapeutic purposes. To understand the involvement of microRNAs throughout mammary cell differentiation, and the association between microRNAs, stem cells and cancer we profiled the expression of all known microRNA in different stages of mammary cell differentiation. Overall design: MicroRNA microarray analysis was based on hybridization between the microRNA and its corresponding probes. RNA sequences were labeled with an affinity tag which allowed detection of microRNAs after hybridization to the chip. Dual color microarray assays were carried out such that each sample (stem cell-like and fully-differentiated) was labeled with either Cy3 or Cy5 dye. Errors introduced by differential labeling were adjusted using dye-swap replicates.