Our preliminary clinical trial showed that consumption of cooked rice of a Japanese common cultivar Yukihikari improved atopic dermatitis associated with a suspected rice allergy, although the underlying mechanisms remain unclear. We hypothesised that the ameliorating effect of Yukihikari on atopic dermatitis is associated with the gut microbiota. BALB/c mice were fed a synthetic diet supplemented with uncooked and polished white rice powder prepared from one of four different cultivars: Yukihikari, rice A (common rice), rice B (brewery rice) and rice C (waxy rice). Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments showed that the composition of faecal microbiota was different between mice fed Yukihikari and those fed rice A. Analysis of the 16S rRNA clone library and species-specific real-time PCR showed that the abundance of Akkermansia muciniphila, a mucin degrader, tended to be lower in mice fed Yukihikari. The incidence of allergic diarrhoea induced by oral administration of ovalbumin in systemically immunised mice was lower in mice fed Yukihikari, albeit with no difference in serum antibodies specific to ovalbumin. In a separate experiment, serum antibody levels specific to orally administered ovalbumin were lower in mice fed Yukihikari. Additionally, the translocation of horseradish peroxidase in isolated segments of ileum and colon tended to be lower in mice fed Yukihikari, suggesting a reduction in gut permeability in mice fed Yukihikari. These data indicate that changes in the gut microbiota of mice fed Yukihikari could be advantageous in the prevention of food allergy.