A 38-year-old woman, who presented with pulmonary embolism associated with thrombi in the main pulmonary arteries and enlarged right-sided chambers, was discovered to have both activated protein C resistance (APCR) and protein S deficiency. She had a heterozygous mutation for factor V Leiden. Especially in young individuals under 45 years of age and in the absence of risk factors, inherited prothrombotic defects should be considered. Hereditary APCR accounts for more thrombotic events than the other inherited deficiencies such as protein C and S and anti-thrombin. The presence of these factors together increases the risk and severity of thrombotic events.