We investigate the possible structures of three-dimensional colloidal crystals formed when these spherical particles are dispersed in a liquid crystal. The case of a strong homeotropic boundary condition is considered here. Their corresponding defect structures in the space-filler nematic liquid crystal are induced by the presence of the spherical surface of the colloids and produce an attraction between colloidal particles. Here, a standard Landau–de Gennes free energy model for a spatially inhomogeneous liquid crystal is numerically minimized to yield an optimal configuration of both spherical colloids and the orientational field. The stable and metastable structures obtained in this work are described and analyzed according to the type of periodic liquid-crystal defect lines that couple the colloidal spheres together. A large range of the spherical size is covered in this study, corresponding to a 5CB-liquid-crystal comparison for assembling micron- to nano-sized colloidal spheres. Multiple configurations are found for each given particle size and the most stable state is determined by a comparison of the free energies. From large to small colloidal particles, a sequence of structures, which range from quasi-one-dimensional (columnar), to quasi-two-dimensional (planar), and to truly three-dimensional, are found to exist.