This book constitutes the refereed proceedings of the Second International Conference on Autonomous Infrastructure, Management and Security, AIMS 2008, held in Bremen, Germany, in June 2008, under the auspices of IFIP. The 13 revised full papers presented together with 8 papers of the AIMS PhD workshop were carefully reviewed and selected from 33 submissions to the main conference and 12 papers for the PhD workshop respectively. The papers are discussing topics such as autonomy, incentives and trust, overlays and virtualization, load balancing and fault recovery, network traffic engineering and analysis, and convergent behavior of distributed systems.