Study design: Retrospective review of patient data. Objectives: (i) To determine the incidence and time of deep vein thrombosis (DVT) under low molecular weight heparin (LMWH) prophylaxis in spinal cord injury (SCI), (ii) to determine the incidence and time of heterotopic ossi®cation (HO) and (iii) to assess a possible aetiologic relationship in the pathogenesis of DVT and HO. Setting: Swiss Paraplegic Centre, Nottwil. Methods: We analyzed the incidence of DVT and HO in 1209 SCI patients (275 ®rst rehabilitations) at the Swiss Paraplegic Centre Nottwil from 1998 to 2000. Clinical ®les and laboratory data were scrutinised for particularities preceding DVT and HO. Results: The incidence of DVT was 6.55% for ®rst rehabilitation compared to only 1.59% in all patients hospitalised. DVT was complicated by pulmonary embolism (PE) in 1.45% and 0.47% respectively. Incidence of HO was 8% for ®rst rehabilitation and 1.82% for all patients hospitalised. In ®rst rehabilitation patients the peak for DVT occurred around day 30 contrary to HO with a peak around day 120. In single patients HO was identi®ed by MRI as a rapidly progressing process. Laboratory pro®les were in¯ammatory in both HO and DVT. Increased physical activity preceding HO was observed in four patients. In two patients acute HO was complicated by ipsilateral DVT. Conclusion: Prophylaxis with LMWH and elastic stockings signi®cantly reduces the frequency of DVT during ®rst rehabilitation in SCI. DVT and HO are both associated with laboratory parameters of non-infectious in¯ammation. The later onset of HO coinciding with ongoing mobilisation, argues for a di erent pathogenetic mechanism. Acute HO of the hip region appears to favour ipsilateral DVT by well known thrombogenic mechanisms.