The role of epithelial polarity and bacterial factors in the control of the innate immune response of airway epithelial cells to Pseudomonas aeruginosa PAK was investigated using a human, nasal cystic fibrosis (ΔF508/ΔF508) epithelial cell line CF15 grown as confluent layers on permeable supports. Addition of PAK to the basal surface of CF15 layers caused significant expression changes in 1525 different genes (out of 12 625 examined), including the cytokines IL-6, IL-8, IL-1β and TNF-α, as well as genes associated with leucocyte adhesion, antibacterial factors, and NF-κB signalling. Confocal microscopy showed that nuclear migration of NF-κB in all CF15 cells was preceded by PAK binding to the basal and lateral surfaces of some cells. Addition of PAK to the apical surface of CF15 monolayers elicited changes in expression of only 602 genes, including 256 not affected during basolateral PAK exposure. Over time, cytokine expression during apical PAK was similar to that exhibited by basal PAK, but the magnitudes during apical treatment were much smaller with little/no nuclear migration of NF-κB in CF15 cells. Furthermore, these responses depended on the presence of flagellin, but not pili on the bacteria. Thus, P. aeruginosa triggered a strong innate immune response that depended on the apical versus basolateral polarity of CF15 cells and the presence of flagellin on the bacteria.