The two-volume proceedings, LNCS 6927 and LNCS 6928, constitute the papers presented at the 13th International Conference on Computer Aided Systems Theory, EUROCAST 2011, held in February 2011 in Las Palmas de Gran Canaria, Spain. The total of 160 papers presented were carefully reviewed and selected for inclusion in the books. The contributions are organized in topical sections on concepts and formal tools; software applications; computation and simulation in modelling biological systems; intelligent information processing; heurist problem solving; computer aided systems optimization; model-based system design, simulation, and verification; computer vision and image processing; modelling and control of mechatronic systems; biomimetic software systems; computer-based methods for clinical and academic medicine; modeling and design of complex digital systems; mobile and autonomous transportation systems; traffic behaviour, modelling and optimization; mobile computing platforms and technologies; and engineering systems applications.