The aim of this study was to determine circadian rhythm abnormalities in patients with acute cerebral infarction and their relationship with prognosis in the chronic phase. The subjects were 50 patients who were admitted within 48 h of onset. Rectal temperature and wrist motor activity were recorded during the acute phase. Time-series data were assayed by MEM spectral analysis. Functional prognosis (degree of handicap) was assessed at 3 months after stroke onset by the modified Rankin Scale. Ambulatory patients tended to exhibit circadian rhythm in rectal temperature and/or wrist activity rhythms, whereas non-ambulatory patients did not (P < 0.001) in the acute phase of ischemic stroke. Our findings suggest the biological rhythms of rectal temperature and wrist activity during the acute stroke phase might be a possible prognostic indicator of their chronic phase.