Cardiac resident stem/progenitor cells are critical to the cellular and functional integrity of the heart by maintaining myocardial cell homeostasis. Given their central role in myocardial biology, resident cardiac progenitor cells have become a major focus in cardiovascular research. Identification of putative cardiac progenitor cells within the myocardium is largely based on the presence or absence of specific cell surface markers. Additional purification strategies take advantage of the ability of stem cells to efficiently efflux vital dyes such as Hoechst 33342. During fluoresence activated cell sorting (FACS) such Hoechst-extruding cells appear to the side of Hoechst-dye retaining cells and have thus been termed side population (SP) cells. We have shown that cardiac SP cells that express stem cell antigen 1 (Sca-1) but not CD31 are cardiomyogenic, and thus represent a putative cardiac progenitor cell population. This chapter describes the methodology for the isolation of resident cardiac progenitor cells utilizing the SP phenotype combined with stem cell surface markers.