The electron transport chain enzyme complex I may play a role in Parkinson's disease (PD) pathogenesis. Association studies considering whether or not complex I-relevant gene polymorphisms contribute to PD risk are discordant. We evaluated four complex I-relevant gene polymorphisms alternatively reported to associate and not associate with PD (tRNA(Gln) T4336C, ND1 T4216C, ND2 G5460A, and the NDUFV2 exon 2 C182T transition). Our study included 111 PD subjects and 106 controls in central Virginia. Individuals with at least one copy of the NDUFV2 182T allele were more likely to report a PD family history than non-carriers, but aside from this no positive associations were found. Indeed, the tRNA(Gln) 4336C variant occurred more frequently in controls. We also observed that individuals in both groups often carried more than one of the assayed polymorphisms, and for the first time show bigenomic polymorphic variation (between nuclear and mtDNA complex I subunit genes) commonly occurs within individuals. In an exploratory sub-analysis, more control than case women had an ND1 4216C, NDUFV2 homozygous 182C compound genotype. Complex I compound genotype variation commonly occurs and may explain why particular complex I gene polymorphisms associate with PD in some populations but not others.