Background: Primary cilia (PC) are non-motile microtubule based organelles present on almost every cell type and are known to serve as critical organizing centers for several signaling pathways crucial to embryonic and postnatal development. Alterations in the Hh pathway, the most studied signaling pathway regulated by PC, affect mammary gland development as well as maintenance of the stem and progenitor cell populations.Results: We developed mouse models with deletion of PC in mammary luminal epithelial, basal epithelial, and stromal cells for evaluation of the function of PC in mammary development via MMTV-Cre, K14-Cre, and Prx1-Cre mediated deletion, respectively. The activity of Cre was confirmed using ROSA26 reporters. Mammary stem and progenitor cells were enriched through growth as mammospheres. Adenovirus-Cre mediated deletion of Ift88 was used to determine a role for PC in this population of cells. Disruption of Ift88 and PC were confirmed in using PCR and immunofluorescent methods. Prx1-Cre; Ift88Del mice demonstrated defects in terminal end buds during puberty. However, these Ift88Del glands exhibited typical terminal end bud formation as well as normal ductal histology when transplanted into wild type hosts, indicating that the phenotype observed was not intrinsic to the mammary gland. Furthermore, no discernable alterations to mammary development were observed in MMTV-Cre- or K14-Cre; Ift88Del lines. These mice were able to feed and support several litters of pups even though wide spread depletion of PC was confirmed. Cells grown in mammosphere culture were enriched for PC containing cells suggesting PC are preferentially expressed on mammary stem and progenitor cells. Deletion of Ift88 in mammary epithelial cells resulted in a significant reduction in the number of primary mammospheres established; however, there was no effect on outgrowth of secondary mammospheres in PC-depleted cells.Conclusions: PC regulate systemic factors that can affect mammary development in early puberty. PC on MMTV- or K14-expressing epithelial cells are not required for normal mammary development or function. PC are expressed at high levels on cells in mammosphere cultures. PC may be required for cells to establish mammospheres in culture; however, PC are not required for renewal of the cultures. © 2014 Mitchell and Serra; licensee BioMed Central Ltd.