The whole spectrum of medicine consists of complex non-linear systems that are balanced and interact with each other. How non-linearity confers stability on a system and explains variation and uncertainty in clinical medicine is discussed. A major theme is that a small alteration in initial conditions may have a major effect on the end result. In the context of non-linearity, it is argued that 'evidence-based medicine' (EBM) as it exists today can only ever be relevant to a small fraction of the domain of medicine, that the 'art of medicine' consists of an intuitive 'tuning in' to these complex systems and as such is not so much an art as an expression of non-linear science. The main cause of iatrogenic disease is interpreted as a failure to understand the complexity of the systems being treated. Case study examples are given and analysed in non-linear terms. It is concluded that good medicine concerns individualized treatment of an individual patient whose body functions are governed by non-linear processes. EBM as it exists today paints with a broad and limited brush, but it does promise a fresh new direction. In this context, we need to expand the spectrum of scientific medicine to include non-linearity, and to look upon the 'art of medicine' as a historical (but unstated) legacy in this domain.