Empty follicle syndrome (EFS) is defined as the failure to aspirate oocytes from mature ovarian follicles during in vitro fertilization. Except for some cases caused by pharmacological or iatrogenic problems, the etiology of EFS remains enigmatic. In the present study, we describe a large family with a dominant inheritance pattern of female infertility characterized by recurrent EFS. Genome-wide linkage analyses and whole-exome sequencing revealed a paternally transmitted heterozygous missense mutation of c.400 G>A (p.Ala134Thr) in zona pellucida glycoprotein 3 (ZP3). The same mutation was identified in an unrelated EFS pedigree. Haplotype analysis revealed that the disease allele of these two families came from different origins. Furthermore, in a cohort of 21 cases of EFS, two were also found to have the ZP3 c.400 G>A mutation. Immunofluorescence and histological analysis indicated that the oocytes of the EFS female had degenerated and lacked the zona pellucida (ZP). ZP3 is a major component of the ZP filament. When mutant ZP3 was co-expressed with wild-type ZP3, the interaction between wild-type ZP3 and ZP2 was markedly decreased as a result of the binding of wild-type ZP3 and mutant ZP3, via dominant negative inhibition. As a result, the assembly of ZP was impeded and the communication between cumulus cells and the oocyte was prevented, resulting in oocyte degeneration. These results identified a genetic basis for EFS and oocyte degeneration and, moreover, might pave the way for genetic diagnosis of infertile females with this phenotype.During in vitro fertilization (IVF) treatment, oocyte retrieval is performed after ovarian stimulation via vaginal puncture. Cumulus-oocyte complexes (COCs), which consist of cumulus cells surrounding the centrally located oocyte, are isolated from the individual's follicular fluid. As was first described by Coulam et al. in 1986, empty follicle syndrome (EFS) is a condition in which the ovarian response to stimulation and follicular development seems normal but no oocytes are retrieved for fertilization.1 EFS can be classified as either false EFS (FEFS) or genuine EFS (GEFS). FEFS is mainly caused by pharmacological or iatrogenic problems; however, the etiology of GEFS, which is responsible for about 33% of EFS, still remains enigmatic. 2 It has been proposed that GEFS is caused by dysfunctional folliculogenesis, ovarian aging, or genetic factors including pericentric inversion of chromosome 2 and LHCGR (MIM: 152790) mutations. 3-7 A retrospective study of 12,359 individuals who underwent assisted reproductive technology (ART) revealed that the prevalence of GEFS was about 0.016%. 8 Without oocytes for fertilization, these individuals fail to achieve pregnancy after a demanding and expensive medical intervention, resulting in stress to both physicians and the individuals themselves.9