The influence of thrombocytopenia on the long-term clinical outcomes has not been thoroughly evaluated in patients with venous thromboembolism (VTE). This study sought to elucidate association of baseline thrombocytopenia with bleeding, recurrent VTE, and mortality risk. We evaluated the influence of baseline thrombocytopenia among 3,012 patients whose baseline platelet counts were available in the COMMAND VTE Registry in Japan with a median follow-up period of 1,219 days. Baseline thrombocytopenia was classified as follows: mild: 100,000 to 150,000/μl; moderate: 50,000 to 99,999/μl; and severe: <50,000/μl. The primary outcome measurement was International Society of Thrombosis and Hemostasis major bleeding, and the secondary outcome measurements were recurrent VTE and all-cause death. There were 167 patients (5.5%) with moderate or severe thrombocytopenia (moderate: 144 patients and severe: 23 patients), 523 patients (17.4%) with mild thrombocytopenia, and 2,322 patients (77.1%) without thrombocytopenia. The cumulative 5-year incidence of major bleeding was markedly higher in patients with moderate or severe thrombocytopenia (moderate or severe 29.4% vs mild: 14.1% vs no thrombocytopenia: 10.6%, p <0.001). After adjusting the confounders, the risk of or thrombocytopenia relative to no thrombocytopenia for major bleeding remained significant (adjusted hazard ratio [HR] 2.15, 95% confidence interval [CI] 1.43 to 3.13, p <0.001). The excess risk of moderate or severe thrombocytopenia relative to no thrombocytopenia was also significant for mortality (adjusted HR 1.54, 95% CI 1.18 to 1.97, p = 0.002), but the risk was neutral for recurrent VTE (adjusted HR 1.05, 95% CI 0.55 to 1.81, p = 0.87). In conclusion, VTE patients with baseline moderate or severe thrombocytopenia had higher risk for major bleeding events and mortality without significant excess risk for recurrent VTE events.