Two experiments were conducted with neonatal pigs to determine the effects of feeding fructooligosaccharides on cecal and colonic microbiota, proliferation of cecal and colonic epithelial mucosa, and short-chain fatty acid concentrations in the cecum. Experiment 1 consisted of feeding neonatal pigs diets containing either 0 or 3 g fructooligosaccharies/L of formula for 15 days and then examining the large intestine for changes in cecal and proximal colonic microbiota; cecal pH; short-chain fatty acid concentrations; morphology of cecal, proximal, and distal colonic epithelial mucosa; gross necropsy; and histopathology. Supplementation with fructooligosacchariudes (FOS) did not alter cell counts of viable bifidobacterial organisms or total anaerobic microbiota, cecal pH, or concentrations of short-chain fatty acids. Cecal mucosal cell density and labeled cells increased with FOS consumption. Proximal colonic mucosal crypt height, leading edge, labeled cells, proliferation zone, and labeling index increased with FOS consumption. Distal colonic mucosal crypt height, leading edge, cell density, labeling index, and labeled cells increased with FOS consumption. Gross necropsy and histopathology found no significan lesions. In Experiment 2, neonatal pigs were fed diets containing either 0 or 3 g fructooligosaccharides/L of formula for 6 days. Fecal samples were collected on the first full day of feeding and on days 3 and 6 after initiation of feeding. On days 1 and 3, concentrations of bifidobacteria were similar between diets; however, on day 6, pigs consuming FOS tended to have greater numbers of bifidobacteria (p = 0.08). These data suggest dietary consumption of FOS will enhance bifidobacteria populations and prevent colonic epithelial mucosa atrophy in neonates fed an elemental diet.