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The mechanochemical method is used to synthesize samples of hydroxyapatite (HA) with substitution of the phosphate ion by silicate and zirconate ions, and substitution of calcium ions by copper ions. In the process of mechanochemical synthesis, carbonate ions and water molecules are incorporated into the structure of HA due to interaction of components of the reaction mixture with air. Intrusion of carbonate into the structure of HA is a competing process with modification of apatite by silicate and zirconate anions; therefore, the composition of the product during synthesis differs from the prescribed one. After annealing of the samples, the composition of the anion-modified HA can be described by the formula Са
10
(РО
4
)
6–
х
(АО
4
)
х
(ОН)
2–
х
, where (АО
4
)
4–
is the modifying anion. Substitution of calcium by copper ions localized at the Са
1
position has been detected. Silver ions are not incorporated into the structure of HA, but are distributed in the apatite matrix in the form of nanocrystals of metallic silver.