The health of the population is the economic potential of a developed country, so the preservation and promotion of public health is a priority now. The state of young people’s health is of the greatest relevance, particularly the students’ health, which is nowadays alarming for the country. The study aims to evaluate the effectiveness of the use of breathing exercises in the physical education of students with health problems on the functional state of the cardiovascular system. Evaluation of the effectiveness of the method of using breathing exercises according to A.N. Strelnikova's methodology and Greer Childers' "Bodyflex" in physical training with students with functional health disorders was based on the results of a comparative experiment conducted at the Department of Physical Education of the Moscow Polytechnic University. The results obtained in the course of the study convincingly prove that the experimental methodology based on the use of breathing exercises in physical education of students with health problems is effective and contributes to the improvement of the functional state of cardiovascular and respiratory systems. Moreover, the results of the study showed that the experimental technique has a positive impact on the well-being and academic achievements of the participants.