The periodontal regenerative techniques using growth factors and stem cells are gaining momentum in periodontics. However, relatively little is known about the biological process and the potential role of direct transplantation of autologous periodontal ligament stem cells (PDLSC) niche in promoting periodontal regeneration.The aim of this is to clinically and to radiographically evaluate the effects of direct transplantation of autologous PDLSC niche (A-PDLSc Ni) in intrabony defects.Among 28 patients, 14 sites in test group were treated with open flap debridement (OFD) followed by direct transplantation of A-PDLSc Ni and other 14 sites in control group were treated with OFD. Clinical and radiographic assessment was done for each site before surgical therapy and at intervals of 3, 6, 9, and 12 months using radiovisiography. For clinical and radiographic parameters, intragroup comparison was made by paired t-test and unpaired t-test for intergroup comparisons.The result showed that significant reduction (P < 0.05) of clinical parameters in both the OFD and A-PDLSc Ni groups. Radiographic parameters such as alveolar crest changes, defect area resolution were not statistically significant in both the OFD and A-PDLSc Ni groups whereas improvement in defect density was statistically significant (P < 0.05) only in the autologous periodontal ligament stem cell niche group.In the present study, treatment of intrabony defect by direct transplantation of autologous periodontal ligament stem cells niche in comparison with OFD showed a significant reduction in probing pocket depth (PPD), gain in clinical attachment level, and there was no gingival recession seen owing to thick gingiva. Radiographically, there was alveolar crest improvement, decrease in defect area, and increase in defect density in A-PDLSC Ni group.