Aim: Studying children of parents with schizophrenia or bipolar disorder, i.e. who are at familial high-risk of developing similar disorders, offers the possibility to identify abnormalities preceding the emergence of mental health disorders during adolescence. This paper reports the rationale and methodology of a single-site electroencephalography-study of the register-based Danish High Risk and Resilience Study–VIA 11. Focusing on event-related electroencephalographic read-outs that have previously been proposed as endophenotypes for schizophrenia, we set out to retrieve these endophenotypes in children at familial high-risk. Method: Event-related cortical responses to repetitive auditory stimuli or visuospatial flanker stimuli will be recorded with 128-channel electroencephalography in eleven-year-old children with one or two parents diagnosed with schizophrenia spectrum psychosis (n>40) or bipolar disorder (n>40) and control children without familial high-risk (n>40). We will test for between-group differences in auditory processing, focusing on the auditory steady-state response and mismatch negativity. We will also assess between-group differences in visually evoked cortical activity implicated in the resolution of a visuomotor response conflict such as P3b potential and lateralized readiness potential. We will further examine whether the individual expression of these electroencephalographic read-outs scale with clinical characteristics.Conclusions: The study will clarify whether the electroencephalographic-derived endophenotypes are only expressed in children of parents with schizophrenia or will also be present in children of parents with bipolar disorder. The multiple electrophysiological-based read-outs of brain reactivity will enable additional exploratory analyses. Together, the study will contribute to current attempts to validate and identify electroencephalographic-based endophenotypes of vulnerability for mental health disorders.