Sudden sensorineural hearing loss (SSHL) is a disease with unknown etiology. Recently, several studies revealed that some inherited prothrombotic risk factors are associated with SSHL in western populations. The objective of this study was to investigate the roles of the two most common genetic prothrombotic factors, the factor V Leiden G1691A and prothrombin G20210A in Taiwanese patients with SSHL. Twenty-four patients diagnosed with SSHL of more than 30 dB on average pure tone audiometry (PTA) and thirty-six healthy subjects without a history of hearing loss were enrolled in this study. Genomic DNA was isolated from peripheral blood leukocytes and the single nucleotide polymorphisms (SNPs) genotyping of factor V Leiden G1691A and prothrombin G20210A were analyzed using the TaqMan genotyping assays. Neither factor V Leiden G1691A nor prothrombin G20210A was detected in SSHL patients or in the control subjects. Both the patient group and the control group exhibited wild-type V Leiden 1691GG and wild-type prothrombin 20210GG. In conclusion, the factors V Leiden G1691A and prothrombin G20210A do not seem to play any role in Taiwanese patients with SSHL. Further studies with a large series of patients are needed to identify other possible candidate genes in order to elucidate the pathogenesis of SSHL.