This volume of the Lecture Notes in Computer Science series contains the papers accepted for presentation at the Third International Conference on Autonomous Infrastructure Management and Security (AIMS 2009). The conference took place in Enschede, The Netherlands, hosted by the University of Twente. AIMS 2009 was organized and supported by the EC IST-EMANICS Network of Excellence (#26854) and co-sponsored by IFIP WG 6.6 and the Strategic Research Orientation of the University of Twente on Dependable Systems and Networks (DSN). AIMS 2009 constituted the Third edition of a single-track and standalone c- ference on management and security aspects of distributed and autonomous systems, which took place initially in Oslo, Norway in June 2007, followed by AIMS 2008 in Bremen, Germany. The theme of the AIMS 2009 conference was “Scalability of Networks and Services,” focusing on how scalable networked systems can be monitored, managed, and protected in an ef cient and autonomous way. The research papers that have been selected for publication in the present proceedings have approached this theme from different perspectives, covering topics such as network resource management, overlays and peer-to-peer networks, network configuration and optimization,and monitoring and visualization.