Participants in the 2008 Academic Emergency Medicine Consensus Conference "The Science of Simulation in Healthcare: Defining and Developing Clinical Expertise" morning workshop session on developing systems expertise were tasked with evaluating best applications of simulation techniques and technologies to small-scale systems in emergency medicine (EM). We collaborated to achieve several objectives: 1) describe relevant theories and terminology for discussion of health care systems and medical simulation, 2) review prior and ongoing efforts employing systems thinking and simulation programs in general medical sectors and acute care medicine, 3) develop a framework for discussion of systems thinking for EM, and 4) explore the rational application of advanced medical simulation methods to a defined framework of EM microsystems (EMMs) to promote a "quality-by-design" approach. This article details the materials compiled and questions raised during the consensus process, and the resulting simulation application framework, with proposed solutions as well as their limitations for EM systems education and improvement.