As mentioned above, associations of different mitochondrial haplogroups with elite athletic status has been reported in Europeans, Africans, and Asians, respectively. However, the functional polymorphisms which are responsible for the previously reported associations between haplogroups and elite athletic status have not been identified. Each mitochondrial haplogroup is divided into several subhaplogroups which are younger branches than the haplogroups in the mtDNA phylogenetic tree. Young branches (subhaplogroups) in the mtDNA phylogenetic tree contain a higher proportion of nonsynonymous substitutions in the protein-coding genes and substitutions in the rRNA and tRNA genes than old branches (haplogroups) (Elson et al. 2004; Ruiz-Pesini and Wallace 2006), since influential variants have been eliminated from the older branches of the tree by ‘purifying selection’ (in evolutionary terms). Thus, subhaplogroup-specific substitutions are more likely to be associated with various health- and performance-related phenotypes. Then, in order to identify the precise mtDNA polymorphisms which associate with elite Japanese athletic status, we analyzed entire mtDNA sequences of 185 elite Japanese athletes from various sports (Mikami et al. 2013). All athletes had represented Japan at international competitions, and they were divided into 100 EMA and 85 SPA. The control group (CON) consisted of 672 Japanese individuals, whose entire mtDNA sequences were registered in our Human Mitochondrial Genome Single Nucleotide Polymorphism Database (http://​mtsnp.​tmig.​or.​jp/​mtsnp/​index.​shtml) (Tanaka et al. 2004). From the analysis of the entire mtDNA of 185 elite Japanese athletes and 672 control subjects, we detected a total of 1,488 mtDNA variants. Among these variants, a total of 311 variants were polymorphisms (minor allele frequency > 1 % in CON), and the frequencies of these polymorphisms were compared among the three groups. Consequently, we found that the EMA displayed an excess of seven polymorphisms, including subhaplogroup D4e2- and D4g-specific polymorphisms, as compared with CON (P < 0.05, Table 10.1), whereas SPA displayed an excess of three polymorphisms and a dearth of nine polymorphisms, including haplogroup G- and subhaplogroup G2a-specific polymorphisms, as compared with CON (P < 0.05, Table 10.1). However, none of these polymorphisms differed significantly between groups after correcting for multiple comparison (false discovery rate q-value > 0.05); a reflection most likely due to a lack of sufficient statistical power. Therefore, replication studies are required to confirm these associations between mtDNA variants and elite athletic performance.