The present study was performed to elucidate the time course of the cerebral and cerebellar blood flows and the significance of SPECT for predicting the outcome in cerebral embolism. 99mTc-hexamethylpropyleneamine oxime (99mTc-HMPAO) SPECT was repeatedly performed in 60 patients with unilateral cerebral embolism. The distribution of 99mTc-HMPAO in the infarct area decreased in the acute phase, increased from 3 h to 22 days after the stroke and then gradually and eventually decreased in the chronic stage. This tendency was observed irrespective of the thrombolytic therapy. The asymmetry index (AI) in the cerebral hemisphere in the first 6 h and later than 30 days correlated significantly with activities of daily living in the chronic stage (p < 0.05). The cerebellar AI after, but not up to 14 days also correlated with the long-term outcome (p < 0.05). In conclusion, a high distribution of 99mTc-HMPAO frequently and transiently occurs in the subacute stage of cerebral embolism. The cerebral and cerebellar asymmetry of the 99mTc-HMPAO distribution is an important predictive value for the outcome; however, the timing of SPECT is critically important.