Hereditary protein S deficiency is one of the natural anticoagulant deficiency causing thrombophilia. Protein S deficiency is caused by a mutation in the PROS1 gene on 3q11.2 and is typically inherited in an autosomal dominant manner. We herein describe a Korean man with protein S deficiency from a novel nonsense mutation of PROS1. The patient was a 47-year-old man with deep-vein thrombosis. No relevant family history was documented. Coagulation test results included a significantly decreased protein S activity at 30%. Molecular genetic analysis targeting PROS1 on suspicion of hereditary protein S deficiency revealed that he was heterozygous for a novel transversion mutation, c.903C>G, in the exon 9 of PROS1. The mutation was predicted to result in premature termination at the codon 301 in the laminin G-type domain (p.Tyr301) of the protein (nonsense mutation). According to a review of the literature and database, the mutation described herein is the first substitution mutation affecting the codon 301 of PROS1.