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There are many methods for regeneration of periodontal ligament damaged by periodontal disease. Although enamel matrix derivative (EMD) is one of the most effective methods, its mechanism is not well understood. We explored how the cell proliferation, differentiation and gene expression of periodontal ligament fibroblasts (HPdLF) are influenced by peptides derived from EMD. In addition, we studied hybridization using microarray analysis. Microarray analysis showed that the expression of genes related to osteogenesis increased with the use of EMD. Our study showed that peptides derived from EMD are beneficial to periodontal ligament cells.