Mosaicism refers to the presence of multiple cell clones with distinct genotypes arising from a single zygote. The phenotype of mosaic individuals depends on the extent of mosaicism, ranging from localised to almost generalised. We report three diagnostically challenging cases with previously unrecognised mosaicism in the tumour predisposition syndromes (TPS) von Hippel-Lindau syndrome, neurofibromatosis type 1 and neurofibromatosis type 2. In all three patients there was a strong clinical suspicion for a TPS; however, no pathogenic variant (PV) was detected in these patients in DNA extracted from blood. With next generation sequencing (NGS) analysis of multiple affected tissue samples of these patients we were able to detect a recurrent PV at varying variant allele fractions. In all three patients, low-grade mosaicism was in retrospect confirmed in normal tissue and blood (variant allele frequency: 1%–7%). Therefore, we conclude that NGS on multiple affected tissues is an effective strategy to detect low-level mosaicism. Identification of previously unrecognised low-grade mosaic cases not only allows for more precise diagnosis and management advice for the index patient, but also accurate genetic counselling for family members.