Background: Genetic variation accounts for ~50% of the variation in endurance performance (1). There is a large maternal component to this contribution (1). Mitochondria have a unique matrilineal inheritance pattern making them a candidate for this component. Previous studies have investigated the association between mitochondrial haplogroup and endurance athlete status (e.g. 2-3). However, the results have been inconsistent. Furthermore, they include associations between haplogroup and strength athlete status. No studies have simultaneously investigated associations between mitochondrial haplogroup, athlete status, mitochondrial DNA (mtDNA) copy number and quantitative measures of endurance and strength. Methods: The major European haplogroups were determined for 407 Lithuanians (84 END, 126 SSP and 197 CON). Haplogroups were classified according to (4) using TaqMan genotyping at positions 4580 G/A, 7028 C/T, 8251 G/A, 9055 G/A, 10398 G/A, 12308 A/G and 13368 G/A. Primer/probe sequences have been previously published with the exception of 9055 G/A for which a custom assay was designed. Individuals with haplogroups atypical for European populations, or with a rare combination of genotypes found in more than one European haplogroup, were classified as others. VO2 max and isokinetic peak torque were assessed using standard protocols. Mitochondrial DNA copy number was assessed by qPCR as a proxy for mitochondrial number. Haplogroup frequencies were compared using Genepop. Results: Overall haplogroup frequencies (Table 1) were similar to published frequencies for Lithuanian populations (5). Haplogroup U was significantly different between END and SSP (p=0.008). Carriers of haplogroup U were 2.5 times more likely by odds ratio to be END than SSP (p=0.005). Haplogroup was significantly associated with mtDNA copy number by ANOVA both before (p=0.014, r2adj=2.64%) and after (p=0.015, r2adj=2.62%) a correction for athlete group. Haplogroup U had the highest mtDNA copy number. However, no associations were observed with VO2 max or isokinetic peak torque. Conclusions: Mitochondrial haplogroup is significantly associated with END status and mtDNA copy number but not with more direct measures of whole body physiology. The high mtDNA copy number of haplogroup U may explain its over-representation in END.