Aim: The aim of this pilot study was to compare the heteroplasmy levels of specific mitochondrial (mt)DNA mutations in human buccal epithelial and whole blood cells in participants with different degrees of predisposition to atherosclerosis. The potential for buccal epithelium to be used for the genetic diagnosis of atherosclerosis using mtDNA mutations was assessed.Methods: Samples of buccal epithelial and whole blood cells were obtained from 134 donors. DNA was extracted from the samples and subjected to polymerase chain reaction and pyrosequencing. The threshold heteroplasmy levels of the mutations m.12315G>A, m.3336T>C, m.1555А>G, m.13513G>A, and m.3256C>T were analyzed in order to assess the potential for using buccal epithelium and whole blood for the genetic diagnosis of atherosclerosis.Results: The threshold heteroplasmy levels of the assessed mitochondrial mutations did not significantly differ between buccal epithelial and whole blood cells.Conclusion: Buccal epithelial cells may be preferable to whole blood cells for analyzing the association of mitochondrial genome mutations with atherosclerosis