In piglets, the development and composition of intestinal microbiota is influenced by dietary factors. A considerable reduction in feed intake during the transition from liquid to solid feed is often accompanied by postweaning diarrhea. Therefore, it is hypothesized that variations in feeding level during weaning may affect intestinal microbial composition. Forty-eight piglets fitted with simple ileal T-cannulas were used to examine the effects of a high (60 g/kg BW) and a low (30 g/kg BW) feeding level on the composition of the ileal and fecal microbiota. The assay diets contained graded inclusion levels of soybean (Glycine max) meal or casein. Bacterial cell numbers of total eubacteria, Lactobacillus spp., and the mainly proteolytic Clostridium leptum, Clostridium coccoides, Enterobacteriaceae, and Bacteroides-Prevotella-Porphyromonas group (Bacteroides group) of feces and ileal digesta were determined by use of real-time PCR. There were no interactions between feeding level and protein source except for the Bacteroides group in ileal digesta. Ileal cell numbers of lactobacilli were increased (P < 0.001) at the higher feeding level. In contrast, ileal cell numbers of Clostridium coccoides were lower (P < 0.001) at the higher feeding level. There were no differences of bacterial cell numbers in feces. Results indicate that feeding level affects microbial composition in the small intestine. Also, sufficient feed intake during weaning encourages proliferation of beneficial bacteria, thereby contributing to improved gut health.