Aim: To investigate the cellular composition and molecular mechanisms of periodontal granulation tissue formation using single‐cell RNA sequencing (scRNA‐seq), aiming to enhance the understanding of periodontal disease pathogenesis and identify potential targets for regenerative therapies.

Materials and Methods: Granulation tissue samples were collected from patients undergoing periodontal surgery ( n  = 3). Fresh tissues were processed into single‐cell suspensions and subjected to scRNA‐seq. The data were integrated and compared with existing datasets from healthy gingiva and periodontal ligament. Computational analyses were performed and validated through immunofluorescence staining.

Results: Ten distinct cell clusters were identified across the samples. Granulation tissue exhibited a higher abundance of immune cells compared to healthy tissues. A novel endothelial cell subpopulation, exclusive to granulation tissue, was discovered and characterised by NOTCH3 expression and involvement in ossification pathways. Additionally, granulation tissue fibroblast subpopulations demonstrated a progenitor‐like state, characterised by extracellular matrix reorganisation and low differentiation, similar to cancer‐associated fibroblasts.

Conclusion: This study identified a novel endothelial subpopulation offering new insights into the disease's pathogenesis and presenting potential targets for regenerative therapies. These findings will help advance the understanding of periodontal disease granulation tissue formation and provide information for the development of materials to modulate specific cellular pathways to improve periodontal disease management.