The recent surge in the network modeling of complex systems has set the stage for a new era in the study of fundamental and applied aspects of optimization in collective behavior. This Focus Issue presents an extended view of the state of the art in this field and includes articles from a large variety of domains where optimization manifests itself, including physical, biological, social, and technological networked systems.PACS numbers: 89.75.k, 87.18.Sn, 87.16.Yc One of the broadest areas of research, optimization has a very long history. It comprises the variational principles in physics and engineering, the survival-of-the-fittest principles that pervade biology and economics, the founding hypotheses of numerous computer algorithms, and the frameworks for addressing the improvement of efficiency in various contexts. Whether a fact or a goal, a natural process or a man-made system, the apparently ubiquitous striving for optimization generates continuing appeal among researchers. But what is new about optimization in networked systems?Real-world systems do not operate isolated from each other. While a neuron can be studied in a laboratory setting, it has not evolved to work independently of the activity of other neurons nor has the brain evolved to work independently from the organism. In a hierarchy of scales, many systems are formed by the interconnection of subsystems that may have different (or even opposing) optimization goals than the global system which they are part of. Expectedly, the structure of these interconnections will influence the global performance and hence complex network research [1, 2] is a key ingredient for studying optimal system behavior (see Fig. 1). Not surprisingly, various structural and dynamical network properties have been explicitly related to the optimization of specific functions (see, e.g., Refs. [3, 4, 5] for early works and Refs. [6,7,8,9, 10] for recent reviews). In this context, there are entire classes of problems, ranging from epidemic spreading [11] to the control of cascading failures [12], which are naturally defined as extremization problems. Others, such as the unexpected robustness observed in some systems, involve no a priory optimization * E-mail address:motter@northwestern.edu † E-mail address:toro@nd.educonditions and yet reveal enhanced properties shaped by the evolution of the system.Optimal behavior is most often connected to a function that the system performs. In numerous cases the function is multi-variate or multi-faceted. For example, the power grid has as its main role the transport of electric energy while minimizing generation and distribution costs and maximizing at the same time reliability and quality of service. 'How network structure influences the global performance of such systems' is probably the question that is posed most frequently in network research. Conversely, the notion of network acts as a unifying theme in systems optimization. Indeed, with the increasing abundance of empirical and theoretical results, numerous optimization FI...