Hepatic sinusoid, the smallest vessel in the liver, plays important roles in hepatic microcirculation. Although the structure of the hepatic sinusoids affects diverse functions of the liver, little is known about morphological alterations in the sinusoids under pathological conditions. In this study, we show that the structure of hepatic sinusoids can be identified three-dimensionally in normal and carbon tetrachloride-injured mouse liver, using the absorption mode of synchrotron radiation micro-computed tomography. We observed that the hepatic sinusoidal structure on tomographic slice images was similar to that on histological images of normal and acutely injured mice. Moreover, centrilobular necrosis and structural alterations of the sinusoids in the necrotic region were detectable on tomographic slice and volume-rendered images of the acutely injured mice. Furthermore, quantitative analyses on 3D volume-rendered images of the injured sinusoid revealed decrease in the volume of the sinusoid and connectivity of the sinusoidal network. Our results suggest that the use of synchrotron radiation micro-computed tomography may improve our understanding of the pathogenesis of hepatic diseases by detecting the hepatic sinusoids and their alterations in three-dimensional structures of the damaged liver.