Zeolite nanocrystals were prepared from three-dimensionally ordered mesoporous-imprinted (3DOm-i) silicalite-1 by a fragmentation method involving sonication and dissolution within a certain pH range. 3DOm-i silicalite-1 with spherical elements with diameters ranging from 10 to 40 nm and a wide range of crystal sizes (100-200 nm, 500-600 nm, and 1-2 μm) was used as the starting material. The highest yield (57%) of isolated nanocrystals was obtained for 3DOm-i silicalite-1 with a crystal size of 100-200 nm and a spherical element diameter of 40 nm. The smallest nanocrystals obtained, albeit in very low yields, had a 10 nm diameter. Preparation of stable silicalite-1 nanocrystal suspensions fragmented from 20 and 40 nm 3DOm-i silicalite-1 was demonstrated. Cryogenic transmission electron microscopy showed that the isolated zeolite nanocrystals can be used as seeds for the epitaxial growth of silicalite-1. An application of these findings was demonstrated: silicalite-1 nanocrystal suspensions were used to deposit seed layers on porous α-alumina disks, which were converted to continuous thin (300-400 nm) films by secondary growth that exhibited both high permeances and separation factors (3.5 × 10 -7 mol m-2 s-1 Pa-1 and 94-120, respectively, at 150 °C) for p- and o-xylene.