A periodic density functional theory (DFT) study of the isomerization reactions of toluene and xylene catalyzed by acidic mordenite is reported. Monomolecular isomerization reactions have been considered and analyzed. The different reaction pathways have been discussed in detail. The use of periodic structure calculations allows consideration and analysis of zeolite electrostatic contributions and steric constraints that occur within zeolite micropores. Major differences in the details of protonation reaction pathways are found when periodic structures are used rather than small cluster models of the Bronsted acidic site. Complex relationships are found between zeolite topology and reaction pathways.