Two trials were conducted to evaluate the effect of different cereals in piglet diets on the jejunal mucosa and the ileal and cecal microbiota during the first postweaning days. In Trial 1, 48 newly weaned pigs (7.95 kg BW; 26 d of age) were individually housed and distributed among 3 experimental diets containing white rice (Oryza sativa), naked oats (Avena sativa), or barley (Hordeum vulgare) as the cereal source. At the start of the trial (weaning; day 0), 12 piglets were slaughtered and sampled to obtain initial reference values for histology and microbiology determinations. Additionally, 4 pigs per treatment per day were slaughtered and sampled at days 1, 2, and 6 postweaning. Villus height (VH), crypt depth (CD), and intraepithelial lymphocytes (IEL) in jejunal mucosa were measured, and microbiota in ileal and cecal digesta were evaluated by RFLP. The Manhattan distances between RFLP profiles were calculated and, for each treatment and sampling day, intragroup similarities (IGS) were estimated. In Trial 2, an additional 48 piglets were used (7.56 kg BW; 26 d of age), and the same experimental procedures were performed except that the 3 experimental diets contained extruded white rice, extruded naked oats, or extruded barley as the cereal source. A reduction in VH was observed in both trials from day 0 to 6 (P < 0.05). In Trial 1 (raw cereals), more IEL and deeper crypts were observed for the barley than for the naked oats based diets (P < 0.05). In Trial 2, no differences among extruded cereals were observed for the histological parameters. In Trial 1, feeding naked oats resulted in lower IGS (increased heterogeneity) of the microbiota in the ileum and in the cecum compared to rice and barley (P < 0.05). In Trial 2, the pigs fed extruded barley had lower IGS in the ileum than those fed extruded naked oats and extruded rice whereas in the cecum, both extruded barley and extruded rice resulted in lower IGS than extruded naked oats (P < 0.05). It is concluded that cereal nature affects the composition of the microbiota and the morphology of the gut mucosa in newly weaned pigs.