Cancer stem cells possess the ability to self-renew and differentiate into specific cells found in tumor types, a characteristic feature of normal multipotent stem cells. These cells harbor within the bulk of tumors and if the tumor suppressor p53 is mutated in these cells, can be more likely to cause relapse and metastasis by giving rise to new tumors. This new paradigm of oncogenesis has been observed in various cancers, including lung cancer. Determining the interaction of critical cellular pathways in the ontogeny of lung tumors is expected to lead to identification of molecular targets for effective therapeutic strategies. To achieve this, it is important to characterize and dissect the differences between the cancer cells with aberrant stem cell like properties and normal multipotent stem cells that contribute to regeneration. This could be accomplished by using cell surface markers unique for certain cell types by employing techniques such as flow cytometry and magnetic bead isolation. This chapter summarizes the isolation process of the resident stem cell Sca1 (+ve), CD-45 (−ve), and CD-31 (−ve) populations for its potential use in assessing correlations between specific p53 gain of function phenotypes in different murine lung cancer models.