The first objective of the present study was to examine the presence of Oxalobacter formigenes (an oxalate-degrading bacterium in the human intestine) according to sex in a large number of Japanese. The second objective was to study the presence of three related genes in Bifidobacterium breve, which is considered to be a new oxalate-degrading bacterim. Fecal samples were collected from 55 male and 37 female healthy volunteers. O. formigenes was detected by a polymerase chain reaction (PCR) and a culture-based method. DNA was amplified by the PCR method including the site of important base sequences of each gene in order to detect oxc, frc, and OxlT. O. formigenes was present in 80% of 54 male and 62% of 34 female subjects in the PCR-based assay, while it was present in 62% of 40 male and 50% of 24 female subjects in the culture-based assay. The partial base sequences of the three related genes in B. breve were determined. The RNA polymerase-binding site in promoters and the rho-independent termination sequence were preserved in oxc and frc. In conclusion, the rate of the presence of O. formigenes was the same as in previous reports. Female subjects showed a 15% lower rate than males. B. breve is considered to be an oxalate-degrading bacterium since it was found to have oxalic acid-degrading ability and three genes involved in oxalate degradation.