The Asian population is thought to have a low risk of venous thromboembolism (VTE), but the epidemiology of VTE in cancer patients remains unclear. The National Health Insurance Research Database of Taiwan was used to find hospitalised patients newly-diagnosed with cancer to determine the incidence of VTE in cancer patients and to identify the risk factors for VTE. Between 1997 and 2005, 497,180 cancer patients were identified. During a median follow-up of 21.3 months (range 0-119.9 months), 5,296 patients developed VTE. The estimated incidence was 185 events per 100,000 person-years. Patients with a prior history of VTE and female patients between the ages of 40 and 80 carried high risk of VTE. The rate of VTE was relatively high in patients with myeloma, prostate cancer, lung cancer, gynaecologic cancers, sarcoma, and metastasis of unknown origin. We developed a risk-stratification scoring system to divide the cancer patients into four discrete risk groups (very low risk, low risk, intermediate, and high risk). The incidence of VTE in each group was 0.5%, 0.9%, 1.5%, and 8.7%, respectively (p < 0.001). This scoring system was validated in a separate patient cohort. In conclusion, VTE is a distinct burden for cancer patients in Taiwan. The risk scoring system could prove helpful in decision-making concerning thromboprophylaxis in cancer patients.