The aim of our study was to investigate the effect of omega-3 fatty acids (FA) on expression of connexin40 (Cx40) in rat aorta during inflammation. Cxs are proteins of gap junction channels which regulate homeostasis and vasomotion through direct intercellular communication. FA are known for their anti-inflammatory and beneficial effects on the cardiovascular system. In 10-day-lasting experiment, we used adult Wistar rats divided into four groups: W(C) – controls, W(FA) - FA in dose 30mg/kg/day, W(L) – application of a single dose of lipopolysaccharide (LPS, 1 mg/kg, i.p), W(L+FA). Cx40 expression was analyzed in aortic tissue using Western blot, its distribution by immunofluorescence and morphometric image analysis. We studied NO dependent relaxation of aorta and NOS activity, together with biomarkers CRP, MDA, NAGA in plasma and CD68 in aorta. Immunofluorescence revealed changes only in endothelial Cx40 spatial expression. In W(L+FA) density of Cx40 spots was decreased when compared to W(L) which increased Cx40 density in comparision to W(C). Total Cx40 expression in aorta of W(L) was significantly higher than in W(C). In W(L+FA), Cx40 expression was lower than in W(L). LPS increased expression of CD68, while its expression was reduced in W(L+FA) group compared to W(L). FA did not affect LPS-induced impairment of NO-dependent relaxation of aorta, and they had no protective effect on NOS activity. FA diet reduced also LPS-induced increase in levels of biomarkers. Our results suggest that endothelial Cx40-gap junctions might represent one of potential targets of the anti-inflammatory effects of FA diet.