The paper discusses the issues of increasing the effectiveness and safety of treatment of a wide range of diseases on the basis of a chronobiological approach to managing the functional state of the body by influencing its biorhythms with a certain frequency of EMF. The approach is based on the following regularities: the principle of the rhythm of biological processes; the principle of conjugation of bioprocesses and biorhythms; and the phenomenon of assimilation of external rhythms by living organisms. According to the principle of rhythm, all bioprocesses have their own biorhythms. Therefore, in case of a disease, a violation of bioprocesses in the body is accompanied by a deviation of their biorhythms from the norm - desynchronosis. Thus, diseases can be treated not only by pharmacotherapy methods, but also by chronophysiotherapy by eliminating desynchronosis. However, there are no hardware-based methods for treating desynchronosis on the market. On the basis of the phenomenon of assimilation of external rhythms and the principle of conjugation of bioprocesses and biorhythms, a method of resynchronization of biorhythms has been developed: treatment of diseases by correcting deviations that have arisen in the biorhythms of a sick organism. The corresponding EMI frequency is used as an external synchronizer. To introduce the method into medical practice, a chronomagnetotherapy apparatus has been created, which simultaneously implements two treatment functions: chronotherapy and magnetotherapy. The chronotherapy function implements a new principle of treatment, the therapeutic factor in which is the frequency component of the EMF from a certain range of biorhythms of a healthy organism. And the function of magnetotherapy is realized by an auxiliary method, the therapeutic factor of which is the magnetic component of the EMF. The device has no side effects on the body, and the effectiveness of treatment on it, in comparison with the methods of pharmacotherapy, increases by 15%.