The unimolecular reactions of protonated α- and β-pinene ions were explored with a combination of collision-induced dissociation tandem mass spectrometry and theory. The two main dissociation reactions in each ion lead to the losses of neutral propene and isobutene. The difference observed between the two ions is a greater relative abundance of propene loss in the case of protonated a-pinene. Both ions were found to dissociate over the same minimum energy reaction pathway, the only difference being the site of initial protonation in the two ions. a-Pinene preferentially protonates at the bridging carbon, while b-pinene can only significantly protonate at the exocyclic double bond. This leads to a lower appearance energy for loss of isobutene, and thus relatively greater m/z 81 fragment ion abundance for b-pinene.