The effects of oral administration of a prebiotic (cellooligosaccharide [CE]) and a combination of a probiotic (a commercial Clostridium butyricum strain) and prebiotics (referred to as symbiotics [SB]) on performance and intestinal ecology in Holstein calves fed milk replacer (MR) or whole milk were evaluated. Forty female calves (experiment 1) and 14 male and female calves (experiment 2) were used in this study. Calves were fed MR (experiment 1) or whole milk (experiment 2) necessary for daily weight gain of 0.3kg based on birth weight in two daily feedings and weaned at 46 days. Calves were divided into a CE feeding group, SB feeding group (only in experiment 1), and control group. The CE and SB groups were fed CE at 5g/day before weaning and 10g/day postweaning. Only the SB group received 108 colony-forming units (CFU) of C. butyricum culture per day. Commercial calf starter was offered for ad libitum intake. Health and feed intake of the animals were monitored daily, and body weight was measured weekly. Fecal samples were analyzed for determination of bacterial community composition by an RNA-based method (sequence-specific SSU rRNA cleavage method) and for organic acid profiling. In 49-day experiments, feed intake, daily gain, and occurrence of diarrhea of the calves were unaffected by either CE supplementation or SB supplementation, and all calves were healthy during each experiment. The fecal bacterial community compositions and the organic acid profiles were not different among groups in experiment 1. In experiment 2, the level of the Clostridium coccoides–Eubacterium rectale group was higher in the feces of CE group than controls at 4 weeks of age and fecal butyric acid concentration was higher (8.0 vs. 12.2 [mmol/kg feces], P<0.05) at that time. There were no differences in prebiotic bacteria (the genera Lactobacillus and Bifidobacterium) between groups at this time point. These results suggested that CE and C. butyricum supplementation have less effect on the performance of healthy calves fed MR. However, prebiotic supplementation seems effective for modulation of the intestinal bacterial community of calves when administered with whole milk.