During an organism's life, adult stem cell pools are maintained by cell division requiring both the genome and the epigenome to be faithfully copied. Due to its high rate of cell division, epigenetic changes are likely to accumulate in the intestinal stem cell (ISC) pool, and indeed age-related changes in DNA methylation status have been shown for whole organ preparations. Moreover, incidence of certain types of cancer, including colorectal cancer, also dramatically increases with age. This has led to the suggestion that alterations of the epigenome may be the underlying cause of the observed increase in tumourigenesis with age. Age related changes also impact on physiological properties of the intestinal epithelium as evidenced by a reduced capacity to absorb essential nutrients like calcium and phosphorus. To study the effect of ageing on the ISC niche in detail we have performed morphological and immunohistochemical characterisation of the intestinal epithelium (2mth versus 22mth old mice) and a functional in vivo regeneration assay on animals of the same age groups. We observed significant changes in the cellular composition of crypt and villus compartments with aging. Furthermore, we detected functional changes in the ability of aged intestinal crypts to regenerate following treatment with chemotherapeutic agent 5-FU. In order to characterize the underlying molecular mechanisms of these age related changes, we developed a novel cell surface marker mediated FACS isolation strategy that allowed us to extract homogenous populations of ISCs from wild type animals that are uncompromised by Lgr5 haploinsufficiency, unlike the commonly used Lgr5-GFP reporter mice. RNA sequencing of ISCs and their niche cells from different age groups (2 mth, 22 mth) showed clear age associated transcriptional changes. To interrogate the causes for these functional and transcriptional changes, we are investigating how the epigenome is altered during ageing in ISCs and their associated niche cells. This strategy will reveal whether age-related changes in intestinal crypts reside primarily in ISCs, supporting niche cells or both.