Post-stroke lower extremity vein thrombosis can be the reason behind complications of embolic nature and death. This study aimed to investigate the influence of provoking factors, frequency and localization of acute thrombosis, post-thrombotic changes in the lower extremity veins during stroke recovery period. The study involved 1315 patients, 885 (67.3%) male and 430 (32.7%) female, ages 18–94 years, mean age 59.23 ± 13.7 years. All participants underwent lower extremity venous duplex scanning in the early and late stages of stroke recovery period. We found no evidence of interconnections between presence of signs of thrombosis and/or its consequences and the pathogenetic variant of stroke the patient had. Acute deep vein thrombosis was diagnosed significantly more often (p < 0.05) in the early stage of stroke recovery period. The frequency of acute lower extremity vein thrombosis was 7.8%, post-thrombotic changes — 5.6%. Isolated lesion of the lower leg veins was the most common complication associated with deep veins (49.6%). We have discovered a significant relationship between the side of lower extremity paresis (plegia) of and the side of deep vein thrombosis (p < 0.001). No relationship was found between lower extremity superficial and deep vein thrombosis and use of anticoagulants and antiplatelet agents (p > 0.05). Excess body weight was associated with damage to the lower extremity proximal veins (p < 0.05). Women had lower extremity vein thrombosis significantly more often (p < 0.05). Repeated lower extremity venous duplex scanning upon admission to the rehabilitation hospital allowed reducing the risk of venous thromboembolic complications that may develop during the stroke recovery period.