Venous thromboembolism (VTE) is a frequent complication in the acute setting after spinal cord injury (SCI). Less is known about the long-term risk of VTE in these patients. It was the aim of this study to prospectively evaluate the short- and long-term risk of VTE in a cohort of patients after acute SCI and during rehabilitation and post-rehabilitation follow-up period. From January 2003 to November 2007 all consecutive adult patients admitted to a Spinal Rehabilitation Unit (RU) after surgical treatment in three Neurosurgical Units for SCI, were enrolled. After an accurate evaluation of their neurosurgical medical records the patients were prospectively evaluated for VTE occurrence. Ninety-four patients (80 males; mean age 40.3 years, SD 15.9) were recruited. All the patients received thromboprophylaxis with low-molecular-weight heparin combined with compressive stockings during hospitalization (median duration 7 months, IQR 4.5-8.8). Over a median follow-up period of 36.3 months (IQR 4.4-48) after SCI, VTE was diagnosed in 22 patients (23.4%) The majority of VTE events were recorded during the first three months of follow-up (34.4 VTE events/100 patient-years in the first 3 months and 0.3 VTE events/100 patient-years thereafter); age over 45 years (HR 8.4, 95% CI 3-23.5), previous VTE (HR 6.0, 95% CI 1.6-23.3) and paraplegia (HR 4.7, 95% CI 1.6-13.7) were independently associated with the occurrence of VTE. In conclusion, the risk of VTE in patients suffering from SCI is high despite the use of thromboprophylaxis, in particular in some patients categories. However, this risk appears to be limited to the first 3 months after the index event.