Goat mammary gland epithelial cells have been used to establish primary and permanent cell lines but to date there is no data on mammary stem cells in this species. The detection and characterization of goat mammary stem cells (gMaSCs) is an important task for a better understanding of the cyclic character of the mammary gland development which will also offer a potential for manipulation of lactation yield and persistency. The objective of the present study was to demonstrate that a subpopulation of MaSCs resides in the goat mammary gland. Mammary tissue from lactating Saanen goats (Capra hircus) was dissociated and processed to a single cell suspension. Using an in vitro colony-forming assay we demonstrated that distinct colony types, which expressed specific lineage markers, arose from unipotent progenitors. Using two different growth media we showed that the frequencies of caprine clonogenic progenitors differed according to growth conditions. Goat epithelial cells were transplanted under the kidney capsule of non-obese diabetic/severe combined immunodeficient (NOD/SCID) mice where they formed organized bilayered structures. Our results indicate the presence of MaSCs in the caprine mammary gland. These data represent the first description of the tissue hierarchy of the goat mammary gland and demonstrate the regenerative potential of goat adult mammary stem cells.