In this work, a multi-agent system (MAS) for supply chain dynamic configuration is proposed. The brain of each agent is composed of a Bayesian Decision Network (BDN); this choice allows the agent for taking the best decisions estimating benefits and potential risks of different strategies, analyzing and managing uncertain information about the collaborating companies. Each agent collects information about customer’s orders and current market prices, and analyzes previous experiences of collaborations with trading partners. The agent therefore performs a probabilistic inferential reasoning to filter information modeled in its knowledge base in order to achieve the best performance in the supply chain organization.