The chapter is focused on the usage of intelligent agents in business process modelling and business process management systems in particular. The basic notions of agent-based systems and their architectures are given. Multiagent systems as sets of multiple interacting software agents, as well as frameworks and methodologies of their development are discussed. Three kinds of architectures of agent-based systems – holons, multi-multi-agent systems and aspect-oriented architecture are described. Examples of already implemented agent-based systems in logistics, transportation and supply chain management are given. The chapter gives an insight into recent business process management systems and their architectures, and highlights several issues and challenges which underpin the necessity for agent-based business process management. Methodologies and implementation of agent-based business process management systems are discussed and directions of future research in this area are outlined.