A new chemical kinetic reaction mechanism has been developed for the oxidation of methylcyclohexane (MCH), combining a new low temperature mechanism with a recently developed high temperature mechanism. Predictions from this kinetic model are compared with new experimentally measured ignition delay times from a rapid compression machine. Computed results were found to be particularly sensitive to isomerization rates of methylcyclohexylperoxy radicals. Three different methods were used to estimate rate constants for these isomerization reactions. Rate constants based on comparable alkylperoxy radical isomerizations corrected for the differences in the structure of MCH and the respective alkane, predicted ignition delay times in very poor agreement with the experimental results. The most significant drawback was the complete absence of a region of negative temperature coefficient (NTC) in the model results using this method, although a prominent NTC region was observed experimentally. Alternative estimates of the isomerization reaction rate constants, based on the results from previous experimental studies of low temperature cyclohexane oxidation, provided much better agreement with the present experiments, including the pronounced NTC behavior. The most important feature of the resulting methylcyclohexylperoxy radical isomerization reaction analysis was found to be the relative rates of isomerizations that proceed through 5-, 6-, and 7-membered transition state ring structures and their different impacts on the chain branching behavior of the overall mechanism. Theoretical implications of these results are discussed, with particular attention paid to how intramolecular H atom transfer reactions are influenced by the differences between linear alkane and cycloalkane structures.