Detailed crystal chemical characterization of human pathological cardiovascular deposits (PCD) was conducted applying wide set of the instrumental methods (XRD, FTIR, Raman, SEM, different chemical analyses). There was some progress achieved in the understanding of it formation mechanism. The obtained data evidence that pathological cardiovascular deposits are presented by non-stoichiometric water-bearing B-type carbonated hydroxyapatite just like other apatites of the human body. But PCD apatite is characterized by higher concentration of B-type carbonate ion (up to ~ 6 wt%) which leads to the increasing influence of the carbonate-ion on the unit cell parameters in comparison with water and other substitutes. Another difference between PCD apatite and other pathogenic apatites of the human body is the smaller variations of the unit cell parameters, caused by smaller variations of the blood chemical composition. It was shown that apatite on the surface of PCD is characterized by the more non-stoichiometric composition compared to apatite inside these deposits. It is assumed that the formation mechanisms of the PCD apatite and the bone apatite may be similar.