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The physical education of students who have a deviation in their state of health requires a joint effort from teachers and doctors. The aim of the study was to substantiate the necessity of swimming classes as an effective means of physical rehabilitation in students with health disorders within the physical education curriculum classes. Students with low-level somatic health (54 students) were grouped into the Basic Group (BG, 27 students) and the Control Group (CG, 27 students). The Basic Group students were offered special swimming classes aimed at their physical rehabilitation. At the beginning of the study and after 24 training classes the authors assessed the somatic health, physical and mental endurance, and adaptation abilities of the autonomic nervous system. Implementation of the method into the curriculum of the BG students resulted in a significant improvement (by 48.1%) of their somatic health. A reliable re-distribution of the students with “poor” and “lower than average” somatic health to the “average” and “higher than average” health group was noted (p < 0.05). The students’ physical characteristics improved by 36.4%. The conducted research proved the necessity of using sectional swimming activities as a means of physical rehabilitation of students with low health.