Biomimetic carbonate–hydroxyapatite (HA) nanocrystals have been synthesized by using the sitting drop vapor diffusion technique, for the first time. The method consists of diffusing vapors of an aqueous solution of NH4HCO3 through drops containing an aqueous mixture of (CH3COO)2Ca and (NH4)2HPO4 in order to increase slowly their pH. This synthesis has been performed in a crystallization mushroom, a glass device developed for protein and small molecules crystallization. The concentrations of the reagents, the final pH and the crystallization time have been optimized to produce pure carbonate–HA as a single phase. X‐Ray diffraction, Fourier transformed infrared spectroscopy, and transmission electron microscopy have been utilized to characterize the synthesized carbonated substituted HA crystals which display nanometric dimensions, plate‐like morphology, and low crystallinity degree, closely resembling the inorganic phase of bones, teeth, and many pathological calcifications. This novel method may prove to be suitable for the study of the interactions and/or the co‐crystallization of hydroxyapatite with minute amounts of biomolecules, polymers, or drugs.