Inherited antithrombin (AT) deficiency (OMIM 107300) is an autosomal dominant disorder and causes a 20-fold increase in the risk of venous thromboembolism. Herein, we describe a case of a novel splice-site mutation in the SERPINC1 gene in a Korean patient with inherited AT deficiency. The patient was a 35-year-old woman who presented with deep vein thrombosis (DVT) and pulmonary embolism and was without a recent history of any precipitating factors. The obtaining of her family history revealed that her mother had an ischemic stroke and a pulmonary embolism and her two sisters both had an episode of DVT during pregnancy. DNA sequencing of SERPINC1 revealed the novel variant IVS1-2A>T (c.42-2A>T), a substitution in intron 1, in the proband and her daughter. The mutation IVS1-2A>T eliminates the acceptor splice-site of intron 1. The present case is the first novel splice-site mutation of SERPINC1 in a Korean family with inherited AT deficiency.