Background: Despite the lack of supporting evidence, unfractionated heparin (UFH) is frequently given to acute ischemic stroke patients. This study was designed to determine the incidence of heparin-induced thrombocytopenia (HIT) during acute stroke and to elucidate the clinical features of stroke patients with HIT. Methods: Of 1,078 consecutive patients with acute ischemic stroke, 392 were given intravenous UFH. Ten of these developed prominent thrombocytopenia without any other underlying etiology; they were suspected of having HIT. These 10 patients were studied retrospectively. The clinical diagnosis of HIT was made according to two published scoring systems. Antiplatelet factor 4/heparin antibodies in the plasma were detected by the enzyme-linked immunosorbent assay (ELISA) and were confirmed by the 14C-serotonin release assay. Results: Eight patients met the criteria for clinical HIT according to both scoring systems. Of these, serological tests were positive in 2 patients only on ELISA and in 2 patients on both assays. The amount of UFH given was greater in the 4 patients with positive serological findings than in the others (p = 0.043). Three patients developed further thromboembolic events, including 1 patient who developed possible cancer-associated thrombosis. Two patients were dead and the remaining 6 patients were dependent at the time of hospital discharge. The clinical severity and outcome of these patients were relatively unfavorable compared to other acute patients. Conclusions: The prevalence of HIT was 0.5% based on both the clinical scoring systems and serological assays. Monitoring for HIT should be included in the medical management of stroke to avoid further complications.