The balance between quiescence and activity of progenitor and stem cell populations is maintained by the ability of these populations to interact with the local microenvironment, often called the niche. Crosstalk between stem cell populations and their niche allows for extrinsic cues from the niche to be integrated with intrinsic properties of the stem cells to sustain progenitor and stem cell identity and concomitantly to execute differentiation programs. The hair follicle has become a powerful model system to explore the interactions between stem cells and their niche in the context of organ remodeling and tissue regeneration due to its accessibility, its well-characterized stem cells and progenitors, and its well-defined anatomy. Furthermore, because hair follicles during the hair cycle in the adult mouse undergo cycles of growth (anagen), regression (catagen), quiescence (telogen) and regeneration in a highly predictive manner, the hair follicle has become an excellent model to study physiological regeneration and morphological transformations in the adult animal. Remarkably, in each phase of the hair cycle, follicles adopt a different morphology and structure, and therefore, the transitions between these phases involve dramatic morphological alterations. This metamorphosis of the follicle during the hair cycle not only requires the exquisite coordination of multiple biological processes and pathways, but also entails the embedded molecular clocks that timely orchestrate the cyclic morphological reorganization of the follicle with stem cell activity, rendering the hair follicle an excellent model system to study stem cell regulation within a complex biological framework. Our research aims to decipher this stem cell regulation and delineate at the molecular level the multiple events underlying the cyclic nature of the hair follicle.