Background: Signal transducer and activator of transcription 6 (STAT6) is a key transcription factor involved in both interleukin-4 (IL-4) and IL-13-mediated biological responses, such as allergies. Recently, we reported that the polymorphism of the STAT6 gene exon 1 was associated with allergic diseases, while another group studied the G2964A variant of the STAT6 gene’s association with atopic asthma. We undertook an association study between these variants of the STAT6 gene and allergic diseases, including atopic dermatitis, bronchial asthma, and food-related anaphylaxis in a Japanese population. Methods: STAT6 gene polymorphisms were genotyped by polymerase chain reaction (PCR) fragment length polymorphism analysis, and PCR-SSCP analysis in 106 allergic and 66 control subjects. Results: The 2964A variant was in significant linkage disequilibrium with the dinucleotide repeat polymorphism, the 13-GT repeat allele of STAT6 exon 1 (p < 0.0000000003). There was no association between the STAT6 2964A variant and allergic subjects in a Japanese population (p = 0.2724). The genotype of 13/15-GT repeat allele heterozygosity was significantly associated with allergic subjects (p = 0.0006), as previously reported. In one major genotype of the STAT6 exon 1 (15 GT repeat homozygosity), wild-type 2964G allele homozygosity was significantly associated with allergic subjects (p = 0.0382). Conclusions: Our findings indicate that in combination the dinucleotide repeat polymorphism of the STAT6 exon 1 gene and the 2964A variant may be useful markers for predicting allergic diseases in a Japanese population.