The entire world has been caught in the SARS-CoV-2 pandemic, which causes COVID-19. It caused a wide spectrum of social problems ranging from financial to public health issues. Because of this, the master thesis focused on discovering new methods of detecting the virus and discovering new risk factors regarding the mitochondrial genome. Mitochondria are commonly targeted by viral infections and because of this the question becomes, are some mitochondrial macrohaplogroups more susceptible to developing more severe symptoms. Using advanced sequencing, we have analysed the mitochondrial DNA samples of patients with severe COVID-19. There was no statistical significance detected regarding the distribution of macrohaplogroups compared to the samples of the general population in Croatia. Besides the distribution of macrohaplogroups we also analysed non-synonimous mutations and heteroplasmic mutations. There was also no significant difference detected in that regard. We found some mutations that have never been described and have to be detected in different studies in order to conduct a thorough analysis on their impact on the mitochondria. Despite there being no new discoveries, these samples are very valuable because of the time period they were obtained in and these results can prove to be very helpful in future studies