Health systems are paradigmatic examples of human organizations that blend a multitude of different professional and disciplinary features within a critically performance environment. Communication failure and defective processes in health systems have a tremendous impact in society, both in the financial and human aspects. Traditionally, health systems have been regarded as linear hierarchic structures. However, recent developments in the sciences of complexity point out to health systems as complex entities governed by non-linear interaction laws, self-organization and emergent phenomena. In this work we review some aspects of complexity behind health systems and how they can be applied to improve the performance of healthcare organizations.