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Background and objectives: Enamel matrix derivative (EMD) is produced from developing porcine tooth buds and represents a complex of low-molecular-weight hydrophobic enamel proteins. EMD is widely applied in periodontal regeneration. Osteoclasts are multinuclear cells, which are responsible for bone resorption. The precursors of osteoclasts, hematopoietic cells, undergo in vivo the process of transendothelial migration before differentiation. EMD is known to affect the process of osteoclastogenesis, but its effect on human osteoclasts precursors after the interaction with activated endothelium was never studied. Materials and Methods: Human umbilical vein endothelial cells (HUVECs)s were seeded in transwell inserts with a pore size of 8 µm and pre-activated by TNF-α and IL-1β for 18 h. Peripheral blood mononuclear cells (PBMCs), freshly isolated from 16 periodontitis patients and 16 healthy individuals, were added to pre-activated HUVECs. Adherent, non-adherent and transmigrated cells were collected and differentiated to osteoclasts by the standard protocol in the presence or absence of EMD. The number of osteoclasts was determined by tartrate-resistant acid phosphatase staining. Results: PBMCs isolated from periodontitis patients have formed a significantly higher osteoclast number compared to PBMCs isolated from healthy individuals (p < 0.05). EMD induced concentration-dependent inhibition of osteoclast formation from PBMCs. This was true for the different PBMC fractions isolated from both healthy individuals and periodontitis patients. Conclusions: Our data show that EMD inhibits the formation and activity of osteoclasts differentiated from the progenitor cells after the interaction with activated endothelium. This might be associated with bone resorption inhibition and supporting bone regeneration in the frame of periodontal therapy.