A mitochondrial Mspl RFLP which was coselected with Marek's disease (MD) resistance in White Leghorn chickens was mapped to the NADH subunit IV. The RFLP was due to a transition, resulting in the change of the low-usage threonine triplet ACT (Mspl- allele) to the high usage triplet ACC (Mspl+ allele). Trait association studies within an unselected strain revealed that the Mspl- allele whose frequency was reduced in MD resistant strains was associated with high body weight and high egg specific gravity (a measure of eggshell thickness). Analysis at three different time points indicated a significant interaction between the mitochondrial genotype and the growth hormone genotype in early but not in late adulthood. The analysis indicates that mitochondrial variants may contribute to phenotypic variation in chickens and that such contributions may be dependent on the genetic background.