Hydroxyapatite (HA), as a bone mineral component, has been an attractive bioceramic for the reconstruction of hard tissues. However, its poor mechanical properties, including low fracture toughness and tensile strength, have been a significant challenge to the application of HA for the replacement of load-bearing and/or large bone defects. Among materials studied to reinforce HA, carbon nanotubes (CNTs: single-walled or multiwalled) have recently gained significant attention because of their unprecedented mechanical properties (high strength and toughness) and physicochemical properties (high surface area, electrical and thermal conductivity, and low weight). Here, we review recent studies of the organization of HA-CNTs at the nanoscale, with a particular emphasis on the functionalization of CNTs and their dispersion within an HA matrix and induction of HA mineralization. The organization of CNTs and HA implemented at the nanoscale can further be developed in the form of coatings, nanocomposites, and hybrid powders to enable potential applications in hard tissue reconstruction.