With the ever growing usage of the world-wide ICT networks, agent technologies and multiagent systems (MAS) are attracting more and more attention. Multiagent systems are designed to be open systems. Therefore, agent technologies aim at the design of agents that perform well in environments that are not necessarily well-structured and benevolent. Looking at the problem solving capacity of MAS, emergent system behaviour is one of the most interesting phenomena one can investigate. However, there is more to MAS design than the interaction between a number of agents. For an effective system behaviour we need structure and organisation. To specify the organisation of a MAS at design time turns out to be a difficult task. If the structure of the MAS needs to adapt to changes in the environment it can turn out to virtually impractical. This paper presents basic concepts of a theory for holonic multiagent systems with the aim to define the building blocks of a theory that can explain organisation and dynamic reorganisation in MAS. In doing so it tries to contribute to solving the well-known micro-macro gap in MAS theories. The applicability of the basic concepts are illustrated with three application scenarios: flexible manufacturing, order dispatching in haulage companies, and train coupling and sharing.