A histological study was designed to determine the influence of flaxseed and/or lactobacilli inclusion in the diet of piglets from 10 days before to 21 days after weaning. The selected inflammatory cell population incidence in the piglet jejunal mucosa was investigated. Significantly higher numbers of myeloperoxidase-positive (P<0.01) and CD163-positive (P<0.001) cells in the jejunal mucosa were recorded on the weaning day and for 7 days after (P<0.001 and P<0.01, respectively) in the flaxseed group compared with the basal diet. The number of intraepithelial lymphocytes was also significantly increased until 3 days after weaning (P<0.001). A prolonged significant increase in the myeloperoxidase-positive cells and intraepithelial lymphocyte numbers in the flaxseed+lactobacilli group was detected. In contrast, the number of CD163-positive cells in the flaxseed+lactobacilli group was significantly lower on the day of weaning (P<0.05) and 3 days after (P<0.01). The same effect was observed in the group with lactobacilli alone during the first 3 days after weaning (P<0.05 and P<0.01, respectively) and these findings indicate down-regulation of CD163 expression in the jejunal mucosa by lactobacilli. The presence of lactobacilli in the diet had a stimulatory effect on goblet cell quantity in the epithelium (P<0.001) and a distinct 50% reduction in the flaxseed group (P<0.01) compared with the basal diet was observed on the weaning day. A significant increase in myeloperoxidase-positive cell number in the jejunal mucosa in the flaxseed+lactobacilli group was the only significant difference (P<0.05 and P<0.01, respectively) found 21 days after weaning in comparison with all the other groups, indicating the pro-inflammatory effect of this feed additive combination. We conclude that dietary supplementation with flaxseed and lactobacilli on the cells of local innate immunity response in the jejunal mucosa in piglets after weaning might be linked with significant anti-inflammatory effects in the jejunal mucosa.