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Injectable biomaterials that can completely fill the root canals and provide an appropriate environment will have potential application for pulp regeneration in endodontics. This study aimed to fabricate and characterize a novel injectable human amniotic membrane (HAM) hydrogel scaffold crosslinked with genipin, enabling the proliferation of Dental Pulp Stem Cells (DPSCs) and optimizing pulp regeneration. HAM extracellular matrix (ECM) hydrogels (15, 22.5, and 30 mg/ml) crosslinked with different genipin concentrations (0, 0.1, 0.5, 1, 5, and 10 mM) were evaluated for mechanical properties, tooth discoloration, cell viability, and proliferation of DPSCs. The hydrogels were subcutaneously injected in rats to assess their immunogenicity. The hydrogels were applied in a root canal model and subcutaneously implanted in rats to determine their regenerative potential for eight weeks, and histological and immunostaining analyses were performed. Hydrogels crosslinked with low genipin concentration demonstrated low tooth discoloration, but 0.1 mM genipin crosslinked hydrogels were excluded due to their unfavourable mechanical properties. The degradation ratio was lower in hydrogels crosslinked with 0.5 mM genipin. The 30 mg/ml-0.5 mM crosslinked hydrogel exhibited a microporous structure, and the modulus of elasticity was 1200 PA. In vitro, cell culture showed maximum viability and proliferation in 30 mg/ml-0.5 mM crosslinked hydrogel. All groups elicited minimum immunological responses, and highly vascularized pulp-like tissue was formed in human tooth roots in both groups with/without DPSCs. Genipin crosslinking improved the biodegradability of injectable HAM hydrogels and conferred higher biocompatibility. Hydrogels encapsulated with DPSCs can support stem cell viability and proliferation. In addition, highly vascularized pulp-like tissue formation by this biomaterial displayed potential for pulp regeneration. [ABSTRACT FROM AUTHOR]