An experimental investigation of structure-performance effects in zeolite catalyzed skeletal isomerization has been carried out. Two structurally different, medium-pore-size zeolites (H-TON and H-FER) with similar acidities were compared in butene skeletal isomerization. While both catalysts proved to be efficient in the test reaction, their deactivation behavior differed substantially. H-FER exhibited significantly higher initial isobutene yields and selectivities, and the catalyst performance was also more stable with time-on-stream. H-TON, on the other hand, needed prolonged operation times in order to achieve product distributions comparable to those of H-FER. The predominant route to isobutene was found to be the monomolecular one, with the bimolecular paths of butene largely responsible for byproduct formation. H-TON was more selective toward disproportionation and, owing to its slightly larger pore dimensions, hydrogen transfer products. H-TON was also observed to be less sensitive to feed reactant than H-FER was, confirming previous theoretically calculated structure effects. Coke belonging to both aliphatic and aromatic families was detected over both zeolites, although the coke formed on H-FER was overall heavier and more aromatic in nature. The tested zeolites could be regenerated by burning of the carbonaceous deposits in air, and both catalysts regained almost all of their initial activities.