AbstractA systematic study of the types of fragmentation undergone by internally excited protonated molecules is presented. Two representative functional groups, ethers and ketones, are selected, and both aliphatic and aromatic substituents are examined. The ions are formed by protonation or alkylation in a chemical ionization source, and caused to fragment by collision at high relative kinetic energy. The prevalence of 1,3‐rearrangements and the breakdown of the even electron fragmentation rule highlight the ion chemistry uncovered here. Specific findings include: (i) electron unpairing reactions associated with alkyl radical loss are common. These are probably energetically less favorable simple bond cleavages and are observed in competition with entropically less favorable elimination reactions. (ii) Alkane elimination is a characteristic reaction, which often occurs by a four‐centered mechanism. Several variations on this reaction type are encountered. (iii) Alkene elimination is another ubiquitous reaction which occurs by a four‐centered mechanism in the systems studied here. Competition between alkene and alkane loss is extremely sensitive to the particular system in hand.