Copper-substituted calcium in hydroxyapatite nanocrystals (CuHAp) were synthesized by co-precipitation method and characterized using various analyses. Structural and chemical characterizations indicate that copper was quantitatively incorporated into the HAp structure, replacing calcium up to 15 at.%. The presence of copper in the HAp structure affected clearly its crystallinity and reduced its crystallite sizes. Rietveld analysis showed a regular decrease of the CuHAp cell parameters a and c. Moreover, this substitution caused a shift in the infrared absorption bands and the nuclear magnetic resonance signals of phosphate groups and a decrease in the thermal stability. Morphological characterizations indicated that the prepared CuHAp consists of extremely thin needle shaped nanocrystals with a greater aggregation, and confirmed the decrease in crystal size that was associated to the increasing in the surface area. The prepared CuHAp nanocrystals showed a high catalytic effect (up to 70%) in the discoloration of the Naphthol Blue Black solutions.