Inhibition of mitophagy is one of the signs of chronic disease pathogenesis. Detection and measurement of mitophagy levels under in vitro and in vivo models provide a better understanding of the role of mitophagy disorder in disease development and serve as prerequisites for creating a clinically applicable system test. The development of such a system is potentially feasible, but taking into account a number of factors that will be discussed in detail in this article. Here it is considered the main models of mitophagy-based test systems and an analysis is carried out showing their advantages and disadvantages. The future potential for the development of mitophagy-based diagnostic test systems is also discussed here.