In many aspects, the epidermis relies on the activity of its stem cells to form the impermeable barrier protecting an individual from environmental insults including UV radiation. Despite significant progress in understanding stem cells, questions remain on their true potency and more especially on their response to injury. In the past few years we have explored the fate of individual clones using unbiased multicolour tracking of single keratinocytes to predict the natural reservoir of cells important for maintaining the interfollicular epidermis in vivo. Mathematical modelling undoubtedly supports a new paradigm where the hair follicle plays a key role in providing committed progrenitors that maintain growth and homeostasis of the epidermis. To further dissect the contribution of hair follicles to skin homeostasis we have designed new animal models to follow hair follicle cycling in vivo and have dissected the mesenchymal epidermal interactions that allow the development of hair follicles and the niche of stem cells. These models increase our understanding of epidermal cells and their environment in health allowing us to predict better their behaviour in response to injury.