The difference between genders in the composition of mouse fecal flora was examined. A polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were performed on the V6-V8 regions of bacterial 16S rDNA obtained from fecal samples at 0, 1, 2, 3, 4, and 8 weeks after the introduction of mice into the laboratory from a mouse farm. Cluster analysis and non-metric multidimensional scaling (NMDS) were then performed. Male and female mice were distributed on opposite sides of the origin of the plane in NMDS at weeks 0, 2, 3, and 8. These results suggest a gender difference in the composition of intestinal flora in mice.