The Claisen rearrangement is a well-known process occurring in condensed phase. In the gas-phase protonated allyl phenyl ethers, propargyl phenyl ethers, and N-allyl aniline produced by positive ion chemical ionization undergo Claisen rearrangement. This reaction has been observed even in the case of odd-electron molecular ions. Phenyl allenyl ether molecular ions actually undergo Claisen rearrangement, producing intense [M - CO](+*) ions. In this investigation, the behavior of protonated benzyloxy indole and some of its derivatives, obtained in electrospray conditions, is described. Low-energy MS/MS experiments carried out on [M + H](+) species show CO loss and an unexpected water loss: both can be justified only by the occurrence of Claisen rearrangement. Deuterium labeling experiments confirm this mechanism. The influence of different substituents in the indole moiety is discussed.