Linseed as a feed ingredient contains a number of constituents, such as mucilage, gel forming polysaccharides, structural carbohydrates and ¿-3 fatty acids, which could have functional properties in relation to maintaining and supporting gastro-intestinal health in post weaning piglets. Intestinal gene expression was studied in weanling piglets fed diets containing either or not linseed or linseed expeller meal. Piglets were either or not orally challenged with an enterotoxigenic strain of E. coli K88. Pairwise comparisons identified several mRNAs expressed significantly different, in particular between treatments C¿ (control, not challenged) and LS¿ (linseed, not challenged) and LS+ (linseed, challenged) and LSM+ (linseed expeller meal, challenged). The intestinal micro-array technique is a promising tool to study the relationship between nutrition and feeding and gut tissue responses under defined conditions.