Objective To evaluate the clinical effects and safety of heparin injection on hemiplegia following urokinase thrombolysis for acute ischcmic cerebral infarction. Methods Fifty-six patients with acute cerebral infarction matched the standards which could be treated with urokinase thrombolysis in our department from January 2004 to January 2008. Among the 56 patients, 36 cases with hemiplegia in 2 h after thrombolysis got their muscle force recover over Ⅲ scale. Then 36 cases were divided into the treated group and control group randomly; 18 cases in the treated group were treated by heparin sodium 1000 U/h intravenously for 5 d. They were monitored for their activated partial thromboplastin time (aPTT) and the injected heparin speed was regulated according to their aPTT to keep their aPTT between 1.5 to 2 times of the control value. The 18 cases in the control group were given oral aspirin 0.1 daily, 24 h after thrombolysis. The 2 groups were compared in the case numbers of hemiplegia reoccurrence and cerebral hemorrhage within 7 d and the National Institutes of Health Stroke Scale (NIHSS) scores. Results Though there were 5 cases with asymptomatic hemorrhagic conversion, there was no hemiplegia case again in the treated group. In the control group, 5 cases suffered from hemiplegia again and 2 cases asymptomatic hemorrhagic conversion. There were less cerebral infarction in the treated group than the control group after 14 d by brain CT. The neurological deficit improvement in the treated group was more efficient in the treated group than in the control group in 14 d. Conclusion The application of heparin for the prevention of hemiplegia in the patients with acute cerebral infarction with muscle recovery after urokinase thrombolysis is safe and effective and shows obvious clinical value when their aPTT is remained 1.5-2.0 times of the normal level.