Aim: The primary goal of this study was to examine whether male students are more physically active than female and to examine the relationship between perceived barriers to physical activity in high school students and levels of their physical activity and propensity for sedentary behavior. Also the aim was to determine whether students with higher level of motivation were also more physically active regardless of the perception of barriers and whether there were gender differences. The secondary goal of this study was to examine relationship between mental health, i.e. mental difficulties, with the level of physical activity and sedentary behavior and to validate croatian version of the Physical Activity Barriers questionnaire and The Strengths and Difficulty Questionnaire. Methods: This study was part of the CRO-PALS study involving 818 high school adolescents in Zagreb. For assessing the level of physical activity was used SHAPES questionnaire which contains two items that require seven days of monitoring of moderate and high intensity physical activity. Sedentary behavior was also estimated through the SHAPES questionnaire which was used to observe the time spent in sedentary behavior. Motivation was assessed through the Croatian version of the questionnaire EMI which consists of 14 motives (dimensions): stress control, revitalization, enjoyment, challenge, social recognition, socializing, competition, disease prevention, health, weight control, appearance, strength and endurance, dexterity, social pressure. Barriers to physical activity were examined by a questionnaire containing 20 items that make two groups: internal and external barriers. Mental health was assessed by the Croatian version of the SDQ questionnaire, which contains 25 items divided into 5 dimensions related to emotional problems, behavioral problems, peer problems, hyperactivity and prosocial behaviors. Results: It was found that male students are more physically active compared to their female peers who report higher tendency to sedentary behavior. What motivates participants the most to exercise are health, appearance, revitalization, and weight control. Internal barriers are a strongest predictor of sedentary behavior. Regardless of the perception of barriers, motivation is the one on which depends change of behavior and participation in physical activity. The tendency to sedentary behavior is associated with higher difficulties of self-assessed mental health.