Although significant progress has been made in controlling the dispersion of spherical nanoparticles in block copolymer thin films, our ability to disperse and control the assembly of anisotropic nanoparticles into well-defined structures is lacking in comparison. Here we use a combination of experiments and field theoretic simulations to examine the assembly of gold nanorods (AuNRs) in a block copolymer. Experimentally, poly(2-vinylpyridine)-grafted AuNRs (P2VP–AuNRs) are incorporated into poly(styrene)-b-poly(2-vinylpyridine) (PS-b-P2VP) thin films with a vertical cylinder morphology. At sufficiently low concentrations, the AuNRs disperse in the block copolymer thin film. For these dispersed AuNR systems, atomic force microscopy combined with sequential ultraviolet ozone etching indicates that the P2VP–AuNRs segregate to the base of the P2VP cylinders. Furthermore, top-down transmission electron microscopy imaging shows that the P2VP–AuNRs mainly lie parallel to the substrate. Our field theoretic simulations indicate that the NRs are strongly attracted to the cylinder base where they can relieve the local stretching of the minority block of the copolymer. These simulations also indicate conditions that will drive AuNRs to adopt a vertical orientation, namely by increasing nanorod length and/or reducing the wetting of the short block towards the substrate.