Peak distortion and baseline perturbations in ion mobility spectra of butyl acetate isomers were caused by fragmentation of product ions during transport through the drift region of an ion mobility spectrometer (IMS). Extensive fragmentation of MH + and M 2H + at atmospheric pressure in air occurred with thermal energy changes ( 3 kT 2 ) of only 0.013 eV and the extent of fragmentation was influenced by the butyl isomer structure. At 150°C, major fragment ions were mass identified by IMS/mass spectrometry for t- and iso-butyl acetates as m/z 57 and for sec-butyl acetate as m/z 61. No fragmentation and only declustering from dimer to monomer ions were observed with n-butyl acetate. Fragmentation in the IMS drift region is proposed to occur by an intermolecular rearrangement mechanism through the monomer ion.