Abstract Background In 2003, the National Policy for Continuing Education in Health (PNEPS) was created as a strategy to train and update workers of the Unified Health System. To be effectively instituted, the Open University of the Brazilian Unified Public Health System was conceived to offer free online courses. But, it was observed that the online educational modules developed were not structural and pedagogically homogeneous. Objective Propose a matrix of criteria and guidelines to support the improvement of the design of instructional modules, investigating three main areas: ergonomics, education and health. Methodology Anasynthesis was the approach to build the evaluation matrix. Results The matrix consists of 29 criteria (Accessibility, Progression Activities, Updating Practices, Self-Analysis and Self-Management, Assessment, Cognitive Load, Student-Centered, Collaboration, Compatibility and Interoperability, Consistency, Knowledge Building, Student Control, Documentation and Help, Aesthetics, Feedback, Flexibility, Error Management, Interactivity, Maintenance, Clear Instructional Goals and Objectives, Motivation, Personalization, Problem Practicing, Critical Reflection, Relevance, Renewable, Safety, Use of Different Paths, Valorization of Knowledge) with 132 guidelines that allows to check if the online self-instructional module meets minimum quality criteria. Five courses produced by the UNA-SUS system were tested and compared with the perception of users of these courses, obtained by the polls for opening and closing the courses. There was an approximation between the evaluations using the matrix and the responses of the surveys of the courses, answered by the users. Results from these surveys were transferred to a user matrix. The Interactivity and Collaboration criteria were considered non-mandatory for self-instructional courses without tutors. Conclusions The matrix is an adequate evaluation tool for self-instructional courses developed for Continuing Education. Key messages The evaluation matrix is adequate to evaluate online self-instructional courses developed for Health professionals qualification. Self-instructed courses could be a good tool for Continuing Education in health, according to students’ perceptions.
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