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Objectives: To foster the development of a privacy-protective, sustainable cross-border information system in the framework of a European public health project., Materials and Methods: A targeted privacy impact assessment was implemented to identify the best architecture for a European information system for diabetes directly tapping into clinical registries. Four steps were used to provide input to software designers and developers: a structured literature search, analysis of data flow scenarios or options, creation of an ad hoc questionnaire and conduction of a Delphi procedure., Results: The literature search identified a core set of relevant papers on privacy (n = 11). Technicians envisaged three candidate system architectures, with associated data flows, to source an information flow questionnaire that was submitted to the Delphi panel for the selection of the best architecture. A detailed scheme envisaging an "aggregation by group of patients" was finally chosen, based upon the exchange of finely tuned summary tables., Conclusions: Public health information systems should be carefully engineered only after a clear strategy for privacy protection has been planned, to avoid breaching current regulations and future concerns and to optimise the development of statistical routines. The BIRO (Best Information Through Regional Outcomes) project delivers a specific method of privacy impact assessment that can be conveniently used in similar situations across Europe.