The usage of clinical pathways to describe and organize the treatment of patients in inter-sectoral care has been established through the last decade. In particular, engaging the patient in the treatment process has become more important. Adequate tools and concepts are needed to improve the integration of patients into inter-sectorial care processes. Personalized dynamic pathways form patient-specific extensions for clinical pathways as a flexible instrument that goes beyond traditional application of pathways. They support customizing care for patient-specific requirements as well as adding patient interaction to the care process. This paper adapts the concept of personalized dynamic pathways and proposes a reference architecture for integrating personalized dynamic pathways into existing inter-organizational healthcare information systems.