The aim of the research was to determine the effect of the health-oriented exercises included in the final part of the physical and sport education on the selected factors of the musculoskeletal system of the female students of the selected secondary school, as well as to point out the diversification and the realization of the innovative contents of the teaching lessons with the health aspect, especially from the point of view of the primary prevention of the female students’ health of secondary school, improving the level of the posture and the overall muscular system. The monitored group consisted of 33 female students of the selected secondary school in Trenčín (Slovakia). The experimental group (EG) A consisted of 17 female students (age = 16.9 ± 1.3 years, height = 168.6 ± 3.9 cm, weight = 57.3 ± 3.4 kg) and the control group (CG) B consisted of 16 female students (age = 16.3 ± 1.1 years, height = 167.3 ± 4.7 cm, weight = 58.9 ± 4.8 kg). From the point of view of the data acquisition methods, in initial, ongoing and final evaluations were applied standardized methods for assessing the posture and the muscular system for physical and medical practice. Subsequently, the applied health-oriented exercises were used in the final part of the physical and sport education for 3 months, 3 times per week, for the duration of 12 minutes. The results significantly showed the improvement of the monitored musculoskeletal system (p < 0.01), as well as the overall muscular system (p < 0.01). Based on the findings, we point out the suitability of including the health-oriented exercises in the teaching process of the physical and sport education with the focus on the musculoskeletal system. This study was supported by VEGA 1/0242/17 Physical activity as prevention of functional disorders related to the musculoskeletal system of secondary school students.