Ten to fifteen percent of medical trainees have academic difficulties, the majority of which are cognitive in nature, including clinical reasoning. Many obstacles impede the rapid identification of clinical reasoning difficulties in medical learners. This article reviews the literature on detection and remediation of clinical reasoning difficulties, and offers specific, practical steps for accurately diagnosing and quickly resolving identified problems with clinical reasoning. Faculties need to become more involved in the development and establishment of tools for encouraging direct observation of the development of clinical reasoning in medical learners, and for strengthening the teachers’ pedagogical competencies.