Zeolites are crystalline alumino-silicates with a wide range of regular and well defined pore sizes and connectivities. The pore sizes are in the size and shape range of many organic molecules. Acidic zeolites have been utilized as catalysts for a wide range of organic transformations in the petrochemical industry, including many shape selective reactions. In shape selective reactions the relative contribution of external vs. internal sites, pore connectivity, and pore size are often critical to the design of effective catalysts. It is usually difficult to clearly determine the relative roles of these critical factors. Reported here is the use of mixed isotopic study using two different sized reactants, one labeled with ¹³C-carbon and one with natural abundance carbon, to elucidate detailed mechanism and effect of zeolite pore structure on a novel bimolecular acid catalyzed reaction. The use of advanced analytical techniques, such as GC-FI-TOF mass spectrometry, MAS ¹³C NMR and imagining SIMS, were critical to the conclusions of this study.