Abstract Background This systematic review aims to summarize the clinical studies on the use of scaffolds in the repair of bony defects. Methods The relevant articles were searched through PubMed database. The following keywords and search terms were used: “scaffolds,” “patient,” “clinic,” “bone repair,” “bone regeneration,” “repairing bone defect,” “repair of bone,” “osteanagenesis,” “osteanaphysis,” and “osteoanagenesis.” The articles were screened according to inclusion and exclusion criteria, performed by two reviewers. Results A total of 373 articles were obtained using PubMed database. After screening, 20 articles were identified as relevant for the purpose of this systematic review. We collected the data of biological scaffolds and synthetic scaffolds. There are eight clinical studies of biological scaffolds included collagen, gelatin, and cellular scaffolds for bone healing. In addition, 12 clinical studies of synthetic scaffolds on HAp, TCP, bonelike, and their complex scaffolds for repairing bone defects were involved in this systematic review. Conclusions There are a lot of clinical evidences showed that application of scaffolds had a good ability to facilitate bone repair and osteogenesis. However, the ideal and reliable guidelines are insufficiently applied and the number and quality of studies in this field remain to be improved.