This contribution focuses on the heterogeneity and complexity of health information technology services and systems in a multi-stakeholder environment. We propose the perspective of process modeling as a method to break out complexity, represent heterogeneity, and provide tailored evaluation and optimization of health IT systems and services. Two case studies are presented to show how process modeling is needed to fully understand the information flow, thus identifying requirements and specifications for information system re-engineering and interoperability; detect process weaknesses thus designing corrective measures; define metrics as a mean to evaluate and ensure system quality; and optimize the use of resources.