Apart from the physiological effects of glyceollins, information regarding their tissue distribution is scarce in the literature. Thus, the aim of this study is to clarify the distribution of glyceollins in rat organs. Glyceollins I and III were orally administered to Sprague-Dawley rats (1.0 mg/kg) with daidzein as control, and their accumulations in organs were investigated by liquid chromatography-time-of-flight/mass spectrometry (LC-TOF/MS). Glyceollins accumulated in intact and conjugated forms in circulatory organs with a Tmax of 0.5 h, in the following order of descending preference: liver, kidney, heart, lung, soleus muscle, and abdominal aorta. The accumulation of hydrophobic glyceollin I was more than 1.5 times higher than that of III. In contrast, daidzein and hydroxy equol were detected only in the liver and kidneys at lower concentrations (1/100 times) than those of glyceollins. In conclusion, prenylated isoflavones, glyceollins, were preferentially distributed in circulatory organs as intact, sulfated, or glucuronidated forms up to 6 h after the intake.