Objective To investigate the influence of intravenous thrombolysis to acute cerebral infarction with cerebral microbleeds (CMB). Methods Eight-nine patients with cerebral infarction in the Neurological Department of the Second Affiliated Hospital of Guangzhou Medical College from January 1st , 2011 to December 31st, 2012 were enrolled in this study. All patients were scanned with MRI and GRE. According to the presence of CMB, the patients were classified into two groups, including CMB group and non-CMB group. Past history of smoking, drinking, hypertension, lacunar infarction, diabetes and leukoaraiosis situation were recorded and risk factors of CMB were explored. All patients were treated with intravenous thrombolysis and rescanned with MRI to compare the total number of CMB 24 hours after thrombolysis. Results In the CMB group, the number of patients with mild CMB decreased and the number of patients with serious CMB increased after thrombolysis. CMB was associated with sex, age, hypertension, lacunar infarction and leukoaraiosis. Conclusions Sex, age, hypertension, lacunar infarction and leukoaraiosis were the risk factors of CMB in acute cerebral infarction. Thrombolysis in acute cerebral infarction augments the incidence of CMB and promotes the hemorrhagic transformation.