Research is an important part of emergency medicine and provides the scientific underpinning for optimal patient care. Although increasing numbers of emergency physicians participate in research activities, formal research training is currently neither part of emergency physician training in Australia nor easily available for clinicians interested in clinical research. In a two-part series, which is targeted at part-time clinical researchers in the ED, we set out and explain the key elements for conducting high-quality and ethical research. Part I addressed ethical and regulatory aspects. In Part II, we describe important elements of research science, and practical elements of research conduct and administration, which form the basis for high-quality research.