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Poly(3-hydroxybutyrate) (PHB) is a biocompatible and biodegradable polymer produced by a microbiological way. The devices from this biomaterial can be used for long-time cultivation and substance testing on cells. Mesenchymal stem cells (MSCs) have a potential to proliferate to different cell types, so the use of MSCs opens up great opportunities for testing drugs. The shape and microstructure of the substrate is known to exert a strong influence for growth and differentiation of MSCs, which imposes special requirements on the design of 3D scaffolds. The aim of this work was to study the possibility of using 3D scaffolds based on porous microspheres of different diameter from PHB to create models of 3D cell growth and further use for testing substances. To produce porous microspheres the double water-oil-water emulsification technique using ammonium carbonate as a blowing agent was used. To produce 3D scaffolds the obtained porous microspheres were immobilized on the PHB film by gluing with chloroform. MSCs isolated from bone marrow of newborn rats and fibroblasts COS-1 were used. For investigation of the growth pattern of MSCs and COS-1 on scaffolds they were analyzed by scanning electron microscopy after three weeks of cells cultivation. The produced 3D scaffolds were able to support growth of MSCs and COS-1 on the scaffolds, on scaffolds from small microspheres cell grew on the surface of microspheres and between them; on scaffolds from large microspheres MSCs grew preliminary on the surface of microspheres. The activity of alkaline phosphatase was studied to test possible MSCs osteogenic differentiation. In osteogenic media the activity of alkaline phosphatase in MSCs isolated from bone marrow was elevated 30-times in comparison with control. However, even in osteogenic medium the activity of alkaline phosphatase of MSCs grown on scaffolds didn’t differ from the control that allow to use PHB microspheres-based scaffolds for long-term cultivation of MSCs of their native phenotype and testing substances on them.