The crystal structure of the deuterated acid form of zeolite Y with adsorbed cyclohexane (similar to 1 molecule/ supercage) has been determined by powder neutron diffraction at 5 K. The structure was refined by the Rietveld least-squares method in the cubic space group Fd3m [a = 24.711(2) Angstrom, R-p = 3.13%, R-wp = 4.28%]. Deuterium atoms were located, in order of decreasing occupancy, on O(3)[33(3)%], O(1)[10(2)%], O(4)[3(3)%] and O(2)[2(3)%]. Approximately half of the adsorbed cyclohexane molecules were located in the chair conformation in the 12-ring window. Energy minimization calculations predict various types of binding sites for cyclohexane in siliceous Y, One type of site is found in the 12-ring window and is in excellent agreement with the position determined from the diffraction analysis. Other binding sites in low-symmetry positions are predicted, where cyclohexane is coordinated to 4-ring and 6-ring windows; these could not be detected by the diffraction analysis, Our calculations suggest that cyclohexane molecules experience a rather flat potential surface in zeolite Y.