Background: Pharmacogenomic Clinical Decision Support Systems (CDSS) are considered to be the most feasible tool for adopting pharmacogenomic testing into clinical routine.

Objective: To discuss important factors for implementing pharmacogenomic CDSS into German hospitals.

Methods: We analyzed two relevant studies. Furthermore, we interviewed data privacy officers of three German university hospitals and examined relevant legal regulations in literature.

Results: There are three major barriers for implementing pharmacogenomic CDSS into German hospitals: (i) the legal uncertainty; (ii) the lack of machine-readable data; (iii) the remaining knowledge gap of both genetics and pharmacogenomics among physicians.

Conclusion: The implementation of passive clinical decision support (CDS) for somatic mutations in the form of structured pharmacogenomic reports might be the most feasible CDS feature for clinicians in German hospitals.