Connexin (Cx)-channels can represent one of targets of omega-3 fatty acids (n-3 PUFA) in protection of cardiovascular system against injury. We investigated the anti-inflammatory effect of 10-day n-3 PUFA intake (30 mg/kg/day for 10 days) on expression of Cx40 isoform in the aorta of Wistar rats injected with a single dose of lipopolysaccharide (LPS, 1 mg/kg, i.p.). LPS resulted in up-regulation of Cx40 expression in the aorta associated with reduced endothelium-dependent relaxation. LPS increased levels of inflammatory markers C-reactive protein and malondialdehyde in circulation as well as NOS activity and CD68 expression in aortic tissue indicating presence of moderate inflammation. N-3 PUFA supplementation decreased expression of both Cx40 and CD68 in aortic tissue and suppressed concentrations of C-reactive protein and malondialdehyde of endotoxemic rats. N-3 PUFA did not improve NO-dependent relaxation of aorta and NOS activity in LPS rats. The results indicate the involvement of Cx40 in development of LPS-induced endothelium-dependent functional impairment of the aorta and partial health benefits of n-3 PUFA diet associated with improved Cx40 expression.