It is widely known that mitochondrial DNA mutations may have a substantial impact on the development and course of different multisystem diseases. However, the mitochondrial genome is highly variable; even in the absence of pathological mutations, it carries important individual traits. Some mitochondrial DNA polymorphisms have been fixed by inheritance for thousands of years; they have phylogenetically developed as mankind has been settling in new places. Up to date, these polymorphisms are arranged into the socalled haplogroups. The purpose of this review is to analyze the recent literature on the relationship of the inheritance pattern of the mitochondrial genome (i.e. haplogroups) to phenotypic features. The structure of mitochondrial DNA can phenotypically manifest itself as the body’s physiological properties, predisposition to one or other type of a sport load, and longevity. On the other hand, the individual mitochondrial DNA structure can influence the risk of developing metabolic disturbances, brain disorders, immune system diseases, mental disorders, inflammation, or sepsis. Many investigations deal with the impact of mitochondrial DNA characteristics on predisposition to cancer and the course of this disease. The influence of mitochondrial DNA characteristics on susceptibility to different treatment modalities, such as transplantation, antiretroviral therapy, etc., deserves special attention. This review not only identifies the most interesting recent investigations, but also considers up-to-date methodological approaches to studying mitochondrial haplogroups. Due to the global disembodied results of an analysis of haplogroups today, it is very important to highlight ongoing studies as widely as possible.