We report here the distribution of VNTRs (variable number of tandem repeats; minisatellites) and polymorphic analysis of SLC6A18, which is a member of the SLC6 Na(+)- and Cl(-)-dependent neurotransmitter transporter family. In this study, DNA was obtained from 300 unrelated individuals and 205 patients with essential hypertension (EH). We then analyzed the VNTRs in the genomic DNA by searching for minisatellites of SLC6A18 using the Tandem Repeat Finder program. Eight novel VNTRs were identified: five of which were polymorphic minisatellites (SLC6A18-MS1, -MS2, -MS4, -MS5, and -MS6) and three of which were monomorphic minisatellites (SLC6A18-MS3, -MS7, and -MS8). Next, we investigated the relationship between EH and four of the polymorphic minisatellites (SLC6A18-MS1, -MS2, -MS4, and -MS6). We excluded SLC6A18-MS5 from the common/rare allele analysis, because most individuals were heterozygous and hypervariable for this locus. There were no significant differences observed in the overall distribution of these minisatellites, which indicates that these polymorphisms are not responsible for EH susceptibility in the Korean population. A segregation analysis of the minisatellites in SLC6A18 was then conducted by analyzing genomic DNA obtained from two generations of five families and from three generations of two families. The five polymorphic minisatellites were transmitted through meiosis following Mendelian inheritance, which suggests that polymorphic minisatellites could be useful markers for paternity mapping and DNA fingerprinting. In summary, we discovered five novel VNTR polymorphisms in SLC6A18; however, these variations were not associated with EH.