One of the inevitable and crucial elements of a physiotherapist’s work, in addition to professional competence, is physical fitness. The aim of the study was to evaluate and compare the level of health and physical fitness of the first year physiotherapy program students in Tartu Health Care College (THCC) and Kaunas College of Applied Sciences (KCAS). The subjects were 20 and 29 physiotherapy students, respectively. The students’ physical fitness has been assessed by the following tests: Hand grip test, Stork test, ACSM’s push up test, Biering–Sorensen test, ACSM’s curl up test, YMCA sit– and– reach test, and Harvard step–test. The physical fitness level of THCC students were average and below average in different categories. Only the endurance of the abdominal muscle of THCC male students was “excellent”. However, the health indicators (BMI and waist-hip ratio) of both gender of THCC remained within normal range. In most tests, both male and female students from KCAS received a good grade and their avarage fitness level was better than students from THCC. Despite the fact that BMI results of KCAS students remained within normal range and did not differ from THCC students result, their waist–hip ratio was higher. This may indicate an increased abdominal obesity and thereby health risk. In conclusion, the fintess level of the first-year physiotherapy students of THCC is not satisfactory that can negatively affect their future health and coping with future work.