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Three-dimensional (3D) cell culture systems are reported to be more physiologically similar to the in vivo state than 2-dimensional (2D) models, which are extensively employed in periodontal research. Herein, we developed a 3D gingival tissue model with both epithelial and lamina propria layers using human gingival epithelial Ca9-22 cells and primary gingival fibroblasts. The epithelial layer of the developed 3D gingival tissue culture was treated with butyrate, a metabolite of oral bacteria, and the treatment induced the release of damage-associated molecular patterns, such as DNA and Sin3A associated protein 130 kDa (SAP130). Taken together, butyrate exposure to the epithelium of 3D gingival epithelial-connective tissue hybrid systems could induce epithelial cell death and the subsequent release of damage-associated molecular patterns.