Baicalin is one of the major bioactive constituents of Scutellariae Radix, but the biotransformation of it is poorly understood. In this paper, the metabolism of baicalin in rat was studied. Nine metabolites including one new compound were isolated and identified structurally. The plausible scheme for the biotransformation pathways of baicalin in the rats was deduced. And the main metabolites were evaluated for their antioxidation and anti-inflammation biological activities for the first time.