In this work, adsorption properties of the UiO-66 metal–organic framework were investigated, with particular emphasis on the influence of structural defects. A series of UiO-66 samples were synthesized and characterized using a wide range of experimental techniques. Type I adsorption isotherms for low-temperature adsorption of N₂ and Ar showed that micropore volume and specific surface area significantly increase with the number of defects. Adsorption of hexane isomers in UiO-66 was studied by means of quasi-equilibrated temperature-programmed desorption and adsorption (QE-TPDA) experimental and Monte Carlo simulation techniques. QE-TPDA profiles revealed that only defect-free UiO-66 exhibits distinct two adsorption states. This technique also yielded high-quality adsorption isobars that were successfully recreated using Grand-Canonical Monte Carlo molecular simulations, which, however, required refinement of the existing force fields. The calculations demonstrated the detailed mechanism of adsorption and separation of hexane isomers in the UiO-66 structure. The preferred tetrahedral cages provide suitable voids for bulky molecules, which is the reason for unusual “reverse” selectivity of UiO-66 towards di-branched alkanes. Interconnection of the tetrahedral cavities due to missing organic linkers greatly reduces the selectivity of the defected material.