These proceedings contain the papers presented at the Third International ICST C- ference on Autonomic Computing and Communication Systems, Autonomics 2009, held at the Cyprus University of Technology, Limassol, Cyprus, during September 9-11, 2009. As for the previous editions of the conference, this year too the primary goal of the event was to allow people working in the areas of communication, design, progr- ming, use and fundamental limits of autonomics pervasive systems to meet and - change their ideas and experiences in the aforementioned issues. In maintaining the tradition of excellence of Autonomics, this year we accepted 11 high-quality papers out of 26 submitted and had 5 invited talks, covering various aspects of autonomic computing including applications, middleware, networking protocols, and evaluation. The wide interest in the autonomic systems is shown by the broad range of topics covered in the papers presented at the conference. All papers presented at the conf- ence are published here and some of them, which are considered particularly intere- ing, will be considered for publication in a special issue of the International Journal of Autonomics and Adaptive Communications Systems (IJAACS). The conference also hosted the First International Workshop on Agent-Based Social Simulation and Au- nomic Systems (ABSS@AS).