Genetic evidence that Toll‐like receptor 4 (Tlr4) is the lipopolysaccharide (LPS) receptor and biochemical evidence that Tlr4 confers LPS responsiveness as determined by activation of NF‐κB and expression of inducible cyclooxygenase 2 have been demonstrated. Saturated fatty acids (SFAs) acylated in lipid A moiety of LPS are essential for biological activities of LPS. It is now demonstrated that SFAs, but not unsat‐urated fatty acids (UFAs), induce NF‐κB activation and expression of COX‐2 and other inflammatory markers in macrophages. UFAs inhibit COX‐2 expression induced by SFAs and LPS. Additional evidence suggests that both SFA‐induced COX‐2 expression and its inhibition by UFAs are mediated through a common signaling pathway derived from Tlr 4. These results represent a novel mechanism by which fatty acids modulate signaling pathways and target gene expression. Whether fatty acids also modulate signaling pathways and target gene expression derived from the activation of other Tlrs remains to be determined.—Hwang, D. Modulation of the expression of cyclooxygenase 2 by fatty acids mediated through Toll‐like receptor 4‐derived signaling pathways. FASEB J. 15, 2556–2564 (2001)