Background <p>The concept of vital pulp therapy (VPT) of immature permanent teeth has evolved in recent years. There has been a great tendency towards investigating new pulp capping materials for perfect imitation for natural dentin-pulp complex formation process and restoring the normal tissue’s characteristics. Therefore, this study aimed to assess the clinical and tomographic outcomes of apexogenesis with human treated dentin matrix (hTDM) compared to mineral trioxide aggregate (MTA).</p> Materials and methods <p>40 bilateral deep carious young mandibular first permanent molars (FPMs) in 20 healthy children aged between 6 and 8 years old were randomly allocated into 2 groups in which the FPMs treated with hTDM and MTA after pulpotomy procedure. The children were followed up clinically at 3, 6, 12, and 18 months. Tomographic evaluation was performed at baseline and 18-month evaluation period.</p> Results <p>The overall clinical success rate was 100% in both groups. Regarding tomographic evaluation, the mean differences in root length, periapical diameter and area were statistically significant in each individual group but without statistically significant differences between both groups.</p> Conclusion <p>Human TDM hydrogel could be considered a promising pulpotomy agent for immature permanent teeth.</p> Trial registration <p>The current clinical trial was recorded at clinicaltrials.gov, NCT06116695, 27/10/2023, Retrospectively registered.</p>