The present study introduced a molecular biological approach to demonstrate changes in the composition of intestinal microbiota in neonatal mice. Female BALB/c mice were fed either a control diet or a diet supplemented with fructo-oligosaccharide (FOS) at 50 g/kg diet, and then mated to male mice. A cultivation-independent approach, denaturing gradient gel electrophoresis (DGGE) of the PCR-amplified 16S rRNA gene, was performed to characterise changes in intestinal microbial populations in pups at 0, 7, 14 and 21 d old and their dams. Comparisons of DGGE profiles were performed using the Dice similarity coefficient and the unweighted pair group method with arithmetic mean (UPGMA) cluster analysis based on numbers, positions and intensities of bands. DGGE profiles differed between dams fed control and FOS-supplemented diets. Although profiles in pups on the day of birth showed a high similarity with dams, profiles in 7-d-old pups differed from dams and showed high similarity to littermates. In 14- and 21-d-old pups, profiles again showed high similarity with dams. DGGE profiles in pups were divided into two large clusters of control and FOS-supplemented diet groups in the range of 0- to 21-d-old, suggesting modulation of intestinal microbiota in infants by manipulation of microbiota in dams. The present study shows a useful technique for demonstrating changes in intestinal microbiota and provides a mouse model for modulation of intestinal microbiota in neonatal life.