X-ray powder diffraction data of zeolite Y were analyzed to reveal the distribution of positions of heavy atoms (Br) of sorbate molecules within the pore system of the zeolite. The complex density distribution obtained was analyzed and interpreted by molecular dynamics (MD) simulations, thus enabling insight into the conformations adopted by, and the dynamics of, the sorbed molecules. The MD simulation suggests that at higher temperatures (between 40 K and room temperature) one of the two bromine atoms of the dibromobutane desorbs from the site in the vicinity of the Na cation, and the molecule becomes much more mobile within the system. This observation is supported by the Fourier maps obtained for the 40 K and room temperature data sets. The best interpretation of the 40 K data is achieved by combining two models, one of which takes into consideration the position of the sorbed molecule straddling two supercages via a 12-ring window, and the second accounts for the interaction with the cations on the S(I), site. The analysis strongly suggests static disorder of the framework atoms being of importance for the low-temperature data.