Spermatogenesis is the process by which spermatozoa are generated from spermatogonia. This cell population is heterogeneous, with self-renewing spermatogonial stem cells (SSCs) and progenitor spermatogonia that will continue on a path of differentiation. Only SSCs have the ability to regenerate and sustain spermatogenesis. This makes the testis a good model to investigate stem cell biology. The Farnesoid X Receptor alpha (FXRalpha) was recently shown to be expressed in the testis. However, its global impact on germ cell homeostasis has not yet been studied. Here, using a phenotyping approach in Fxralpha(-/-) mice, we describe unexpected roles of FXRalpha on germ cell physiology independent of its effects on somatic cells. FXRalpha helps establish and maintain an undifferentiated germ cell pool and in turn influences male fertility. FXRalpha regulates the expression of several pluripotency factors. Among these, in vitro approaches show that FXRalpha controls the expression of the pluripotency marker Lin28 in the germ cells.