For the majority of hypertensive cases, no gene or combination of genes and environmental factors clearly leading to hypertension has been identified. Studies to identify "hypertension" genes have focused on the assessment of markers and candidate genes in the nuclear genome. In this study, we have chosen to assess the mitochondrial genome as a site of mutations possibly contributing to susceptibility to hypertension in black Americans who have progressed to end-stage renal disease (H-ESRD). The mitochondrial genomes of 58 H-ESRD and 58 normotensive individuals were systematically analyzed by means of a high-resolution restriction analysis. After stratification by the presence or absence of an African continent-specific Hpal site gain at bp 3,592, differences in the frequencies of mitochondrial DNA (mtDNA) restriction variants in both groups were examined by chi-square analyses. A total of six variants was identified with significant differences in one or both cohorts. An A10398G Ddel mutation in the ND3 gene was significantly increased in the H-ESRD cohort (H-ESRD, P = 0.048; normotensives, P = 0.20), as was an HaeIII T6620C/G6260A double mutation in the CO1 gene (H-ESRD, P = 0.05; normotensives, P = 0.48). The remaining four variants were a G2758A mutation in the 16SrRNA gene (identified by Rsal), T10810C in the ND4 gene (identified by Hinfl), a G7028A/T7055C double mutation in the CO1 gene (identified by Alul), and finally, a A10086G mutation in the ND3 gene (identified by Taql; also causing an Asn→Asp amino acid change). The Rsal and Hinfl variants were in strong linkage disequilibrium with the Hpal site and not amenable to further analysis. After correction of all P values for multiple comparisons, the ND3 A10086G (Asn→Asp) mutation shown by Taql remained statistically significant (P = 0.0036) in the H-ESRD cohort, not in the normotensive cohort. To the best of our knowledge, this is the first report of an increased prevalence of mitochondrial gene variants in hypertensive individuals. In addition, we have identified single-nucleotide polymorphisms in flanking regions of these genes. Although replication and further assessment are necessary, the current results support our hypothesis that mtDNA may account for a portion of hypertensive cases in black Americans with ESRD. © 2001 by the National Kidney Foundation, Inc.