The Saskatchewan Ministry of Health has committed to a multi-million dollar investment toward the implementation of Lean methodology across the province's healthcare system. Originating as a production line discipline (the Toyota Production System), Lean has evolved to encompass process improvements including inventory management, waste reduction and quality improvement techniques. With an initial focus on leadership, strategic alignment, training and the creation of a supportive infrastructure (Lean promotion offices), the goal in Saskatchewan is a whole health system transformation that produces "better health, better value, better care, and better teams." Given the scope and scale of the initiative and the commitment of resources, it is vital that a comprehensive, longitudinal evaluation plan be implemented to support ongoing decision-making and program design. The nature of the initiative also offers a unique opportunity to contribute to health quality improvement science by advancing our understanding of the implementation and evaluation of complex, large-scale healthcare interventions. The purpose of this article is to summarize the background to Lean in Saskatchewan and the proposed evaluation methods.