Endolymphatic sac tumors (ELSTs) are very rare and locally aggressive low-grade neoplasm of endolymphatic system origin, which are associated with von Hippel-Lindau (VHL) disease. Evidence suggests that the specific VHL alteration influences the phenotype. Because of the rarity of ELSTs, only a small number of cases have been subjected to molecular genetic analysis. The correlation between ELSTs and the genotype of VHL remains unclear. Herein, we reported a case of ELST with VHL gene analysis who presented with a family history of VHL disease. The radiologic, histologic, and immunohistochemical features of the tumor were typical of ELST. Using the polymerase chain reaction-single-strand conformation polymorphism sequencing techniques, a germline mutation was identified as IVS1 + 1G→A at position 553 + 1. The mutation found in this case has not been previously reported in ELSTs. It is hoped that the study would contribute to a better understanding of ELSTs and the correlation between ELSTs and the genotype of VHL.