The influence of intravenous drug abuse (IVDA) on native arteriovenous fistula thrombosis (NAT) in chronic hemodialysis patients is unknown. We conducted a retrospective study of 123 chronic hemodialysis patients incarcerated in a male prison in Mid-Taiwan. All patients were dialyzed three times per week, 4 h per session. The development of NAT was compared in patients with a history of IVDA (42, 34.1%) and those without (81, 65.9%). A total of 36 patients experienced one or more NAT episodes in 6 years and 29 (80.6%) of them had a history of IVDA. In these 29 patients, 22 (75.9%) relied on repeated thrombectomy or thrombolysis therapy to maintain patent vascular access. In Kaplan-Meier survival analysis, patients with a history of IVDA were prone to develop NAT (log-rank, P < 0.001). The result of Cox regression suggested that a history of IVDA, independent of diabetes, was associated with the development of NAT. Patients with a history of IVDA, even after IVDA has stopped, were still prone to develop NAT and vascular access infection.