It is thought that, as we age, damage to our stem cells may lead to diminished stem cell pool function and, consequently, a reduced organ regeneration potential that contributes to somatic senescence. Stem cells have evolved many antitoxicity mechanisms, and certain mechanisms may be utilized to isolate hematopoietic stem cells. One method exploits the activity of the ATP-binding cassette/G2 transporter to efflux Hoechst 33,342 and results in a stem cell population known as the side population (SP). The SP subset represents a remarkable enrichment for hematopoietic stem cells and provides an opportunity to re-evaluate age-based changes in hematopoietic stem cells. We report here that the frequency of SP cells steadily increases with age, as does the proportion of Lin(-)/Sca-1(+)/c-kit(+) cells that is capable of Hoechst efflux. Phenotyping, progenitor, and long-term repopulation assays have indicated that SP cells in older mice are still stem cells, albeit with a lower homing efficiency than SP cells from younger mice. Analysis of apoptosis within SP cells has revealed an apoptosis-resistant population in SP cells from old mice. Gene expression analysis has determined that SP cells from old mice have a reduced expression of apoptosis-promoting genes than SP cells from young mice. This increase in SP cells with age seems to be an intrinsic property that may be independent of the age of the microenvironment (niche), and our data might provide some clues as to how this alteration in the proportion of stem/progenitor cells occurs. A possible selection-based mechanism of stem cell pool aging is discussed.