Primary cilia (PC) are solitary, sensory organelles that are critical for several signaling pathways. PC were detected by immunofluorescence of cultured cells and breast tissues. After growth for 7 days in vitro, PC were detected in ∼70% of breast fibroblasts and in 7-19% of epithelial cells derived from benign breast (184A1 and MCF10A). In 11 breast cancer cell lines, PC were present at a low frequency in four (from 0.3% to 4% of cells), but were absent in the remainder. The cancer cell lines with PC were all of the basal B subtype, which is analogous to the clinical triple-negative breast cancer subtype. Furthermore, the frequency of PC decreased with increasing degree of transformation/progression in the MCF10 and MDA-MB-435/LCC6 isogenic models of cancer progression. In histologically normal breast tissues, PC were frequent in fibroblasts and myoepithelial cells and less common in luminal epithelial cells. Of 26 breast cancers examined, rare PC were identified in cancer epithelial cells of only one cancer, which was of the triple-negative subtype. These data indicate a decrease or loss of PC in breast cancer and an association of PC with the basal B subtype. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials. © 2010 Yuan et al.