Integrating heterogeneous application systems in healthcare is needed to support clinical work, patient-centric care, regional interoperability and utilization of both valuable legacy systems and new technologies. The integration process is quite complicated, and must be supported by flexible integration processes and methods. The integration methods should support evaluation and specification of different integration approaches and technologies on many different interoperability levels. We introduce a process for specifying many integration decisions for a given integration situation. The process is part of an integration method, which is validated in PlugIT project in Finland.