The study "Molecular Neuropathology 2.0" (MNP2.0) offers an integrated histo-molecular diagnosis including the detection of potential therapeutic targets for a large cohort of pediatric patients with primary CNS tumors. After obtaining parental and/or patient consent, in this study germline DNA analysis of all study subjects bridges the gap between scientific genetic analysis and medical care. The study's workflow takes into consideration the conditions of a multicenter study, legal stipulations, as well as the need for close interdisciplinary cooperation. Here we present an elaborate workflow illustrated by four case studies of patients diagnosed with different cancer predisposition syndromes (CPS). The diagnosis of a CPS and subsequent family analysis are of substantial importance for all presented cases. Germline analysis within the ongoing MNP 2.0 study provides information about the prevalence and distribution of underlying germline mutations in a large population-based cohort of pediatric neuro-oncology patients. In addition, results of this study have the potential to identify high risk tumor entities-or molecular subgroups for underlying CPS.