Recent studies have been showed that various adult tissues contain cells by Hoechst dye efflux, as so-called ���Side Population (SP) cells��� which are highly enriched to differentiate into several types of cells including hematopoietic cells. This study is to characterize the molecular phenotypes of SP cells from adult heart and bone marrow. We isolated SP cells from adult heart and bone marrow of mice (4~5weeks) after staining Hoechst dye by a dual laser-FACS analysis. And then RNAs were extracted from these cells. We performed Real Time RT-PCR with Oct-4, embryonic stem cell marker, Flk-1 and Tie-2, bone marrow derived SP cell markers, Csx/Nkx2.5 and Myosin heavy chain, cardiac specific markers and compared with those of P19 cells, known as embryonic stem cells. Population of SP cells was higher in hearts(0.40 % of total nucleated cells) than bone marrow(0.04% of total nucleated cells). Real time RT-PCR showed that Csx/Nkx2.5, Myosin heavy chain, Desmin were more expressed in the heart-derived SP cells than bone marrow-derived SP cells and P19 cells. Oct-4 was expressed in heart and bone marrow-derived SP cells, but not in P19 cells. Flk-1 and Tie-2 were evenly expressed in three kinds of cells. SP cells from heart and bone marrow-derive show the phenotypes to differentiate into cardiomyocytes. Heart derived SP cells have cardiac-specific activity than bone marrow derived SP cells even though they have similar properties of Hoechst dye efflux.