The primary objective was to demonstrate the different risk factors among patients presenting with usual and unusual site venous thromboembolism (VTE). The secondary objectives were to compare clinical characteristics and outcomes in each group. This was a retrospective observational cohort study. Patients admitted in Chiang Mai University Hospital who were diagnosed with VTE during January 2010 through December 2012 were included and classified into two groups: the usual and unusual site VTE. The usual sites of VTE included pulmonary embolism and lower extremity deep vein thrombosis. Clinical characteristics, risk factors, treatment, recurrence, bleeding rates, and deaths were collected. There were 165 patients included in the study, 82 in usual site group and 83 in unusual site group. Patients in usual site group were older than unusual site group (mean 58 vs. 50 years, P = 0.003) and were more symptomatic (89 vs. 49.4%, P < 0.001). The higher proportion of patients in usual site group had prolonged immobilization (22.0 vs. 2.4%, P < 0.001), prior surgery (12.2 vs. 1.2%, P = 0.005), and a history of chemotherapy (25.6 vs. 3.6%, P < 0.001). Local inflammation was significantly more common in unusual site group (0 vs. 8.5%, P < 0.001). The recurrent VTE and major bleeding rates were not statistically different between groups. The 3-year mortality rate was significantly higher in usual site VTE group (73.1 vs. 57.8%, P = 0.049). The study revealed the different risk factors and clinical characteristics between usual and unusual VTE sites.