This article describes a "Mastery Rubric" (MR) used to design both the curriculum and the assessments in a new two-year certificate programme intended to train physicians in clinical research skills. The MR for clinical research skills is built around a set of core research skills: critical review of literature; articulation of research objective; development of research design; development of analysis plan; implementation of the study; implementation of the analysis plan and presentation of results. Four distinct levels of performance are described for each skill: beginning, novice, competent and proficient. This rubric outlines and provides a path to mastery of the clinical research skills the certificate programme was designed and funded to target. Using the rubric to design the curriculum ensures that courses will provide instruction in key domains, promotes assessment that demonstrates development in the target skills and knowledge, and encourages reflection and cognitive self-monitoring in the students. It is a flexible, criterion-referenced definition of "success" for students as well as the programme itself. The criteria are characterised in terms of the skills, habits of mind and organisational principles that can foster excellence in clinical research, but the approach can be generalized. (Contains 1 table.)