In this study, we investigated the effect of supplementation of the maternal diet with linseed oil [rich in 18:3(n-3)] on fatty acid composition, mucosal architecture, and mast cell regulation of barrier function in piglet ileum. Sixteen sows were fed a lard (LAR)- or a linseed oil (LSO)-based diet during gestation and lactation. Fatty acid composition of maternal RBC at parturition and of milk at d 14 of lactation were determined. Fatty acid composition, villous-crypt structure, and permeability to horseradish peroxidase in Ussing chambers after mast cell degranulation were determined in the ileum of piglets at d 0, 7, and 28. At d 0, 18:3(n-3) and 20:5(n-3) levels were higher, but 22:6(n-3) and 20:4(n-6) levels were lower in both maternal RBC and piglet ileum of the LSO group. Levels of 18:3(n-3) were also higher in the milk of LSO sows. Levels of 18:3(n-3) were higher in LSO piglet ileum at d 7 and 28. Moreover, at d 28, 20:4(n-6) ileal levels tended (P= 0.09) to be lower in LSO than in LAR piglets, in parallel with a lower mRNA expression of Δ5 desaturase. LSO piglets had shorter villi at d 0 and shorter crypts at d 7 compared with LAR piglets. The effect of mast cell degranulation on ileal permeability decreased with age in both groups but reached a minimum sooner in the LSO group (d 7) than in the LAR group (d 28). In conclusion, linseed oil supplementation of the maternal diet profoundly modifies the fatty acid composition, structure, and physiology of the offspring ileum. J. Nutr. 139: 1110–1117, 2009.