Background & objectives Our study aims to provide the diversity of stem cell use for non-malignant, non-haematological diseases in India through the lens of clinical trials. Methods A PRISMA approach was used to evaluate the safety and efficacy of stem cell use for the period 2001-2021 in India. The outcomes were measured using each disease category, types of stem cells, the origin of stem cells, safety, and efficacy. Results Of the 9206 studies screened, 61 studies that were relevant to stem cell use for non-malignant diseases were included for analysis. Autologous stem cells (75%) were used predominantly compared to allogenic stem cells (18.33%), followed by mixed type (6.67%). Use of bone marrow-derived stem cells (51%) was dominant, followed by melanocytes (19%), adipose (7%), haematopoietic (12%), and (11%) other types of stem cells. The study revealed 37 randomized clinical trial studies conducted in the government research hospital compared to the non-government. Interpretation & conclusions Maintaining the gold standard for stem cell therapy requires randomized clinical trials with large sample sizes, control groups, failures, adverse effects, etc. It is important to have a monitoring and regulation system in stem cell clinical research activities with enough preclinical data and repeated exchanges between the bench and the bedside.