The direct metal-catalyzed [1,3]-transposition of allylic alcohols and allylic silyl ethers is a synthetically useful isomerization process that occurs via [3,3]-sigmatropic rearrangement induced by high oxidation state oxometal complexes. The isomerization requires only a catalytic amount of promoter, and high chirality transfer can be achieved. Thus, it bears a significant potential to become a powerful tool in multistep synthesis. Although [1,3]-transposition of allylic alcohols has been known since the late 1960s, the development of synthetically useful protocols that allow for a high level of regio- and stereoselectivity control and their synthetic applications have emerged only recently. This tutorial review summarizes recently developed regioselective [1,3]-transpositions of allylic alcohols and silyl ethers and their applications to natural product synthesis.