This book constitutes the thoroughly refereed post-proceedings of the International Workshop on Coordination, Organization, Institutions and Norms in Agent Systems, COIN 2006, held as two events at AAMAS 2006, the 5th International Joint Conference on Autonomous Agents and Multiagent Systems in Hakodate, Japan, and ECAI 2006, the 17th European Conference on Artificial Intelligence in Riva del Garda, Italy. This volume is the second in a series focussing on issues in Coordination, Organizations, Institutions and Norms (COIN) in multi-agent systems. The 23 papers in this volume are extended, revised versions of papers presented at the two workshops that were carefully selected during two rounds of reviewing and improvement. The papers are organized in topical sections on modelling and analyzing organizations, modelling and analyzing institutions, normative models and issues, norm evolution and dynamics, as well as autonomy, coordination and social order.