Mitochondrial DNA encodes the genetic information necessary for mitochondrial function. In humans, mitochondrial DNA spans 16,569 base pairs while representing a small fraction of the genetic material in humans. Due to their higher mutation rates compared to nuclear DNA, Mitochondrial DNA mutations are emerging as promising biomarkers for assessing disease predisposition and progression. This in-silico analyzes the correlation between Mitochondrial DNA mutations and two conditions: Leigh syndrome, a severe neurodegenerative disorder, and carotid atherosclerosis, a major cardiovascular disease. We focus on five single nucleotide variants (SNVs) m.14459G>A, m.13513G>A, m.12315G>A, m.1555A>G, and m.15059G>A to explore their roles in both diseases. Our findings suggest that mutations m.14459G>A, m.1555A>G, and m.15059G>A contribute to the pathogenesis of both conditions. In contrast, m.12315G>A is linked to MELAS syndrome and carotid atherosclerosis. Interestingly, the m.13513G>A mutation is associated with Leigh syndrome but negatively correlated with atherosclerosis, suggesting a potential protective effect. These SNVs could serve as targets for diagnostic and therapeutic approaches, enhancing our understanding of the genetic basis of these diseases.