We sequenced all exons and exon-intron junctions of the flavin-containing monooxygenase 3 (FMO3) gene from 3 Japanese individuals and their family members, who were case subjects that showed low FMO3 metabolic capacity among a population of self-reported trimethylaminuria Japanese volunteers (n=50). We found three novel single nucleotide polymorphisms (SNPs) (g. 20752 A>G, g. 27400 G>A, and g. 30308 C>T) causing an amino acid substitution and stop codons, Asn114Ser in exon 4, Trp388Stop in exon 7, and Gln470Stop in exon 9, respectively. The Trp388Stop and Gln470Stop also presented together with known SNPs, Val257Met and Glu158Lys, respectively, in the same alleles of the FMO3 gene to form novel haplotypes. These sequences are as follows: 1) SNP, 060825Shimizu004; GENE NAME, FMO3; ACCESSION NUMBER, AL021026; LENGTH, 25 base; 5'-TATCCAGTGTAAA/GTAAACATCCTGA-3'. 2) SNP, 060825Shimizu005; GENE NAME, FMO3; ACCESSION NUMBER, AL021026; LENGTH, 25 base; 5'-CCAGTCCCGCTGG/AGCAGCACAAGTA-3'. 3) SNP, 060825Shimizu006; GENE NAME, FMO3; ACCESSION NUMBER, AL021026; LENGTH, 25 base; 5'-TGTAGTCCCTACC/TAGTTTAGGCTGG-3'.