The definition and implementation of inter-department and inter-enterprise value chains requires the integration of staff and organisational units as well as the technological integration of involved IT systems. While for simple document-based standard processes suitable solutions already exist, a continuous methodology to model cooperative inter-organisational business processes and their transformation to adequate IT architectures is still missing. Objective of this paper is to develop a modeling methodology for selected classes of typical cooperation problems. Considering a cooperative service scenario as example, this methodology is described in detail and evaluated.