Gymnastics Pilates is an affordable and full-fledged training method. It is often used in the system of rehabilitation after trauma. At the same time, information about the influence of Pilates gymnastics on the functional state of those engaged, especially female freshmen, is not enough in accessible literature. The aim of our investigation was to evaluate Pilates (strength-oriented) lessons effectiveness on higher educational establishments first-year student’ morphofunctional state. Some factors, characterizing first-year students (girls), studying at higher educational establishments and doing Pilates (strength-oriented), morphofunctional state are studied in the article. Anthropometric measurements, dynamics functional tests fulfillment results (Harvard step-test, timed expiratory capacity test, Ruffier-Dixon test) and physical training level, in comparison with group of girls, doing aerobics, are also investigated here. On the whole, monitoring results of the morphofunctional research and physical training level showed aerobics and Pilates lessons positive influence on the physical and functional state of the organism, because both kinds of gymnastics include aerobic loading, contributing to cardiorespiratory system function level increase (results of Ruffier-Dixon test, timed expiratory capacity test and respiratory excursion dynamuics). As it had been expected, such systematic lessons led to working capacity and physical training levels increase, defined by long jump length, push-ups and body flexion/extension dynamics. Participants of both groups (girls) became “slimmer”, the fact is proved by body mass and hip circumference decrease. But the said characteristics increase appeared to be more evident in the experimental group. Pilates (strength-oriented) and aerobics lessons influence physical training level positively and contribute to first-year students’ morphofunctional characteristics increase. The received results have shown greater effectiveness level of Pilates lessons, as compared to aerobics ones. So, Pilates lessons can be suggested as recommended choice among many other methods, allowing students’ health preservation and increase. When planning exercises by Pilates gymnastics, it is necessary to take into account the initial level of the morphofunctional state of those engaged. In order to optimize the training process, it is necessary to carry out a comprehensive monitoring of the status of engaged students, which includes not only pedagogical tests, but also physiological studies.