HIV infections are mainly acquired by mucosal transmission, through oral, rectal, or genital mucosa. Epithelial cells (EC) are the first cells encountered by HIV during infection through sexual transmission and breastfeeding. EC express several receptors critical for both primary HIV infection and secondary transmission. The regulation of co-receptor expression correlates with changes in susceptibility to infection by HIV-1 strains with different tropism. Moreover, inflammatory responses at mucosal surfaces after HIV-1 transmission may influence disease outcome. In the present study, we analyzed the effect of the accessory HIV-1 Nef protein on mucosal EC, using unstimulated or IFN-γ-stimulated HEp-2, T24, and Caco2 cell lines as models for homeostatic or inflamed mucosal tracts. We found that Nef significantly upregulated the expression of CXCR4 on the Caco-2 cell surface and the expression of galactosylceramide on the T24 cell surface. In addition, Nef significantly upregulated IL-6 production by T24 and Caco-2 cells, and TNF-α release by all three cell lines analyzed. Notably, Nef abrogated the IFN-γ-induced modulation of co-receptor expression and cytokine secretion. Our findings suggest that Nef differently regulates co-receptor expression and cytokine secretion at the epithelial level, depending on the anatomical derivation of the cells and the inflammatory status.