Diffusion of water and ethanol in silicalite has been studied in large crystals (70 μm × 30 μm × 15 μm) synthesized via a fluoride mediated route. The near-perfect hydrophobic silicalite (F-) crystals have very few internal silanol defects and, as a result, display water and ethanol transport behavior that is uncontaminated by these defects. The transport diffusivity (Dt) of ethanol is higher than that of water at the same sorbate activity. However, this difference is due to the difference in the shape of the isotherms. The thermodynamically corrected diffusivity (D o) of water is almost an order of magnitude higher than that of ethanol reflecting the difference in molecular size. Estimates of the permeability/permselectivity/separation factors for ethanol/water separation based on the present kinetic and equilibrium data for the fluoride synthesized crystals are compared with the values observed for traditional silicalite membranes. The present diffusivity values for fluoride synthesized silicalite are similar to the values for regular silicalite (OH-) derived from uptake rate measurements but much smaller (by more than four orders of magnitude) than the self-diffusivities derived from PFG-NMR measurements. This result is consistent with the results of other measurements of the diffusion of small molecules in silicalite which suggest that, in macroscopic measurements, the rate of intra-crystalline transport is controlled by the sub-structure (extensive twinning), rather than by diffusion in the ideal MFI micropores. In this situation microscale measurements such as PFG-NMR will lead to erroneously high estimates of transport rates and therefore of permeability and permselectivity. © 2012 Elsevier Inc. All rights reserved.