Physical education is considered to be a favorable context for accomplishment of important educational outcomes and promotion of physical activity in children and youth. The real scope of physical education instruction largely depends on student motivation. Self-determination theory, as a specific macrotheory of motivation, offers a rewarding framework for understanding student motivation in physical education instruction. The paper presents the basic tenets of self-determination theory, the most important studies in the domain of physical education and didactic and methodical implications. Two mini-theories within the self-determination theory are analyzed in more detail, the cognitive evaluation theory and the organismic integration theory. Empirical verification of the theoretical tenets indicates the existence of typical motivational profiles of students in physical education instruction, the basic psychological needs as mediators of influence of social and interpersonal factors on student motivation, followed by the importance of motivational climate, students' goal orientations and teaching style for self-determination of students' behavior in physical education instruction. Didactic and methodical implications refer to the need for developing a more flexible curriculum of physical education, encouraging a motivational climate, task-focused goal orientations, and, especially, encouraging the perceived moving competence of the student.