A central component of competency-based medical education is a framework of higher-order and more fundamental competencies whose purpose is to focus instruction and learning. In the language of the learning sciences, many of these competencies are complex cognitive-perceptual or cognitive-motor skills. Competency-based medical education has been criticized for being reductionistic, that is, for focusing on atomistic skills and failing to capture the essence of professional activities as manifested by complex, integrated capabilities. The value of identifying fundamental skill components is supported by theory and evidence from the learning sciences, however. Complex skills are constructed from fundamental, component skills. Proficient performance of the former is achieved as components are refined and integrated during repeated performance of the skill in a realistic context and as feedback on performance is provided. Competency-based medical education does not propose specific methods for teaching competencies. The learning and instructional sciences, however, posit a number of conditions for learning that support the acquisition of simple skills and their flexible integration into complex capabilities. Learners' motivation and self-regulation skills will also have an impact on the extent to which they engage in learning processes that result in the integration of knowledge and skills into complex competencies.