Increasing evidence has suggested that bronchioalveolar stem cell (BASC) is the progenitor cells of lung cancer stem cells. However, the mechanisms by which self-renewal of BSACs is controlled and how BASCs turn into cancer stem cells still remains to be unknown. In the present study, we successfully isolated bronchioalveolar stem cells (BASCs) from mouse lung using FACS. These BASCs were characterized by clonal growth, self-renewal and high capacity for differentiation, suggesting that these BASCs are indeed stem cells. We investigated the microRNA (miRNA) expression profile of these BASCs using miRNA array and quantitative RT-PCR. We discovered that BASCs possessed a unique miRNA profile, with altered expression of several microRNAs, such as miR-142-3p, miR-451, miR-106a, miR-142-5p, miR-15b, miR-20a, miR-106b, miR-25, miR-486, in BASCs compared to control cells. Our results suggest that microRNAs might play important roles in maintaining the self-renewal capacity of BASCs, and suggest the intriguing possibility that aberrant expression of microRNAs could involved in turning BASCs into lung cancer stem cells.