Background: German university hospitals have started to establish molecular tumor boards in order to enable physicians to make molecular-guided decisions.

Objective: Our aim was to describe the organizational structure and procedures which are currently supporting the molecular tumor boards of five German university hospitals.

Methods: We conducted semi-structured interviews with experts of five university hospitals between December 2016 and February 2017.

Results: We observed heterogeneity in both the organization of genetic testing and the management of the molecular tumor boards among the five hospitals. They used free-text documents in most of their support procedures rather than machine-readable documents.

Conclusion: There are three potentialities to support the process from genetic testing to reporting within the molecular tumor boards: (i) standardized pipeline to integrate automated variant calling and annotation; (ii) tools supporting the experts in creating their reports and presentations and (iii) implementing pharmacogenomic CDSS into clinical routine.