The beta(2)-adrenergic receptor (B2AR) is a G protein-coupled cell surface receptor that is the key target for the beta(2)-agonist drugs used for bronchodelation in asthma and chromic obstructive pulmonary disease. To detect four SNPs with amino acid variations in the B2AR gene, we used the electronic microchip assay (NanoChip system), DHPLC and sequencing. Genomic DNA samples were obtained from the blood of 84 Japanese healthy volunteers. In sum, the agreement rates of the first data set with the final agreement data (allele calls) were 99.7% (328/329), 99.2% (243/245) and 96.7% (325/336). The percentages of no allele designation (ND) were 2.06% (7/336), 2.75% (7/252), and 0.00% (0/336) for the NanoChip system, DHPLC, and sequencing, respectively. As a result of SNP genotyping, we found three samples that might have a novel haplotype. Furthermore we identified the novel haplotype by a simple technique combining the NanoChip system and allele-specific PCR. These results indicated that NanoChip system was the useful method for clinical SNP genotyping and/or haplotyping because of its accuracy, simplicity and versatility.