Female BRCA1/2 mutation carriers affected with breast and/or ovarian cancer may develop new tumor deposits over time. It is of utmost importance to know the clonal relationships between multiple tumor localizations, enabling differentiation between multiple primaries or metastatic disease with consequences for therapy and prognosis. We evaluated the value of targeted next generation sequencing in the diagnostic workup of BRCA1/2 mutation carriers with ≥2 tumor localizations and uncertain tumor origins. Forty-two female BRCA1/2 mutation carriers with ≥2 tumor localizations were selected. Patients with inconclusive tumor origin after histopathological revision were 'cases'; patients with certain tumor origin of ≥3 tumors served as 'controls'. Tumors of cases and controls were analyzed by targeted next generation sequencing using a panel including CDKN2A, PTEN and TP53, hotspot mutation sites for 27 different genes and 143 single nucleotide polymorphisms for detection of loss of heterozygosity. Based on prevalence of identical or different mutations and/or loss of heterozygosity patterns, tumors were classified as 'multiple primaries' or 'one entity'. Conventional histopathology yielded a conclusive result in 38/42 (90%) of patients. Four cases and 10 controls were analyzed by next generation sequencing. In 44 tumor samples, 48 mutations were found; 39 (81%) concerned TP53 mutations. In all 4 cases, the intra-patient clonal relationships between the tumor localizations could be unequivocally identified by molecular analysis. In all controls, molecular outcomes matched the conventional histopathological results. In most BRCA1/2 mutation carriers with multiple tumors routine pathology work-up is sufficient to determine tumor origins and relatedness. In case of inconclusive conventional pathology results, molecular analyses using next generation sequencing can reliably determine clonal relationships between tumors, enabling optimal treatment of individual patients.