Self-determination Theory (SDT), designed by Edward Deci and Richard Ryan, serves among the current major motivational theories in psychology. SDT research has been conducted in many areas, among which are education and health care, but its applications in medical education are rare. The potential of SDT to help understand processes in medical education justifies this Guide. SDT is explained in seven principles, one of which is the distinction of three innate psychological needs of human beings: for competence, for autonomy and for relatedness. Further, SDT elaborates how humans tend to internalise regulation of behaviour that initially has been external, in order to develop autonomous, self-determined behaviour. Implications of SDT for medical education are discussed with reference to preparation and selection, curriculum structure, classroom teaching, assessments and examinations, self-directed learning, clinical teaching, students as teachers and researchers, continuing professional development, faculty development and stress among trainees.