The purpose of the present study was to determine the clinical significance of deep venous thrombus (DVT) in legs diagnosed by ultrasonography in patients with paradoxical brain embolism. The authors performed ultrasonography on the legs of 67 consecutive patients who were diagnosed as having paradoxical brain embolism. We compared the clinical background between DVT-positive and DVT-negative groups, and between hemiplegic-side DVT and non hemiplegic-side DVT groups. DVT were detected in 27 (40%) of all patients. Patients were significantly older in the DVT-positive group (p = 0.044). National Institutes of Health Stroke Scale (NIHSS) scores on admission were worse in the DVT-positive group (p = 0.066). Time from the onset of brain embolism to performance of ultrasonography was longer in the DVT-positive group (p = 0.068). DVTs were detected in hemiplegic-side legs in 14 of 19 patients with hemiparesis. NIHSS score on admission was significantly worse in the hemiplegic-side DVT group (p = 0.018). Period between the onset of brain embolism and performance of ultrasonography was longer in the hemiplegic-side DVT group (p = 0.174). In conclusion, DVTs detected by ultrasonography may be de novo thrombi acquired after the onset of brain embolism.