We present a study on the hydrophobization of spin-on Silicalite-1 zeolite films through silylation with trimethylchlorosilane. Microporous and micro-mesoporous Silicalite-1 films were synthesized by spin coating of suspensions of Silicalite-1 nanozeolite crystallized for different times. Ellipsometric porosimetry with toluene and water adsorbates reveals that silylation decreases the porosity and makes the films hydrophobic. The decrease in porosity depends on the exposed surface area in the pores. Water contact angle measurements confirm the hydrophobicity. Fourier transform infrared spectroscopy reveals that the trimethylsilyl groups are chemisorbed selectively on isolated silanols and less on geminal and vicinal silanols due to steric limitations. Time-of-flight secondary-ion mass spectroscopy and in situ ellipsometry analysis of the reaction kinetics show that the silylation is a bulk process occurring in the absence of diffusion limitation. Electrical current leakage on films decreases upon silylation. Silylation with trimethylchlorosilane is shown to be an effective hydrophobization method for spin-on Silicalite-1 zeolite films.