This chapter aims to develop an instrument for analyzing system deficits – conceptualized as persistent problems. It explores the iterative method by applying it to two new care practices: patients with medically unexplained physical symptoms (MUPS), and the development of psychotherapy through the internet. The iterative method consists of a historically informed system analysis: features that may be seen as the strongholds of the current system but that are said to have negative side-effects are identified. The systemic reproduction of these negative side-effects can be unraveled by analyzing how new or innovative practices give shape to their agency in relation to their direct environment. The chapter presents the theoretical and methodological considerations, leading to a five-step method for systematically unraveling system deficits – conceptualized as persistent problems. It discusses the stories of, and reasoning behind, the new care practices and how systemic problems manifest themselves. Finally, the chapter focuses on the merits of the method applied.