Bone defects that cannot heal with normal bone tissue metabolism in medicine are usually treated with metal implants that provide mechanical support to nearby tissue during the regeneration process. Drawbacks of conventional implants are the possibility of an immunologic reaction to foreign tissue and need for a postoperative process where the inert implant is removed after complete bone regeneration. Bone tissue engineering dedicates great attention to the development of bone scaffolds based on biomaterials that actively participate in bone tissue metabolism due to properties similar to natural tissue. The ideal scaffold should be biocompatible and bioactive, which means that the organism does not recognise it as foreign material and it forms physicochemical bonds that promote bone healing with tight attachment to bone tissue. Additionally, it is essential that the scaffold is degradable with biological remodelling process to nontoxic components, while providing mechanical and structural support to damaged tissue the whole time. Calcium phosphates (CaP), due to their similarity to the inorganic component of bone tissues, are the most researched biomaterial for bone substitute applications. With a biomimetic approach, use of aqueous invertebrates’ skeletons as a biogenic source, it is possible to synthesise bone substitutes that biochemically, mineralogically and structurally resemble the human bone. Besides Ca2+, PO43- and OH- ions, bone calcium-phosphate materials consist of numerous ions that have a great effect on the bone tissue properties. With biodegradable polymer materials, it is possible to affect the CaP properties and synthesise a composite scaffold that resembles inorganic-organic composite material of natural human tissue. Within the research of this doctoral thesis, magnesium and strontium substituted CaP scaffolds are synthesised by a hydrothermal reaction at 200 °C after 48 h. Using the calcium-carbonate structure of the cuttlefish bone, ammonium dihydrogen phosphate (NH4H2PO4), strontium nitrate (Sr(NO3)2), magnesium chloride hexahydrate (MgCl2×6H2O) or magnesium perchlorate (Mg(ClO4)2) as reagents, biphasic three-dimensional highly porous scaffolds based on hydroxyapatite (HAp) and whitlockite (WH) are obtained. Composite scaffolds are prepared by a vacuum impregnation of poly(ε-caprolactone) to the surface of the CaP matrix. The effect of Mg2+ and Sr2+ ions content on the compositional and morphological properties of scaffolds was studied by means of X-ray powder diffraction, Fourier transform infrared spectroscopy, thermogravimetric analysis and scanning electron microscopy (SEM) with energy-dispersive X-ray analysis. The addition of Mg2+ affects the formation of new crystalline phase, WH. Structural refinements performed by the Rietveld method indicate that Mg2+ and Sr2+ were preferentially incorporated into the WH phase structure. SEM micrographs of prepared samples showed that the interconnected highly porous structure of the cuttlefish bone was completely maintained after the hydrothermal synthesis. Mg2+ ions reduce the dimension of surface microspheres characteristic for hydroxyapatite. Mechanical analysis results of compression tests showed a positive impact of the WH on the mechanical properties of CaP scaffolds. The thin surface layer of poly(ε-caprolactone) covers the scaffold surface evenly, enters the structure of spherical clusters and, in comparison to CaP scaffolds, enhances the mechanical properties of composite scaffolds by one order of magnitude. Cell viability tests proved that substituted CaP scaffolds are not cytotoxic. In vitro cell cultures with human mesenchymal stem cells (hMSC) are conducted on CaP and composite scaffolds in osteogenic medium for 21 days. Immunohistochemical staining showed that Mg-CaP scaffolds with the HAp : WH wt. ratio of 90 : 10 and 70 : 30 exhibited higher expression of collagen type I and osteocalcin than the pure HAp scaffold. Calcium deposition was confirmed by Alizarin Red staining. The positive effect of Mg2+ ions on the differentiation of stem cells on porous 3D scaffolds was also confirmed by quantification of gene expression inherent to osteogenic activity (alkaline phosphatase, bone sialoprotein and dental matrix protein) with real-time quantitative polymerase chain reaction analysis. In comparison to composite scaffold substituted with Mg2+, composite scaffold cosubstituted with Mg2+ and Sr2+ showed higher expression of collagen I and the positive effect of strontium on the early stage of stem cells differentiation.