Excess iron deposition in the liver is known to be hepatotoxic and may exacerbate liver injury. However, little is known about iron distribution in the lobule because of the lack of a highly sensitive detection method. The aim of this study is to determine iron distribution in the lobule of human liver by means of synchrotron radiation X-ray fluorescence (SRXRF) microscopy. Mapping of the trace elements was done with use of SRXRF microscopy and compared with the results of staining by Berlin blue and oxidative stress markers. Iron deposits were distributed predominantly in periportal hepatocytes in the normal liver in a decreasing gradient from the periportal area to the perivenous area. This distribution was consistent with the formation of oxidative stress markers, suggesting that hepatocytes in the periportal area may be predominantly primed by iron-induced free radical damage even in normal liver. On the other hand, iron deposits in the periportal area were more intense than those in the centrilobular area in both the liver with chronic hepatitis C and the cirrhotic liver. In conclusion, elemental mapping by SRXRF microscopy was a highly sensitive method for the detection and mapping of elements such as iron and copper in liver sections.