Background Microfracture is a type of bone marrow stimulation in arthroscopic cartilage repair. However, the overall concentration of the mesenchymal stem cells is quite low and declines with age, and in the end the lesion is filled by fibrocartilage. The aim of this research was to investigate a novel method of enhancing microfracture by determining whether low-energy shock waves in microfracture holes would facilitate cartilage repair in a rabbit model.Methods Full-thickness cartilage defects were created at the medial femoral condyle of 36 mature New Zealand white rabbits without penetrating subchondral bone. The rabbits were randomly divided into three groups. In experimental group A, low-energy shock-wave therapy was performed in microfracture holes (diameter, 1 mm) at an energy flux density (EFD) of 0.095 m J/mm2 and 200 impulses by DolorClast Master (Electro Medical Systems SA, Switzerland)microprobe (diameter, 0.8 mm). In experimental group B, microfracture was performed alone. The untreated rabbits served as a control group. At 4, 8, and 12 weeks after the operations, repair tissues at the defects were analyzed stereologically, histologically, and immunohistochemically.Results The defects were filled gradually with repair tissues in experimental groups A and B, and no repair tissues had formed in the control group at 12 weeks. Repair tissues in experimental group A contained more chondrocytes,proteoglycans, and collagen type Ⅱ than those in experimental group B. In experimental group B, fibrous tissues had formed at the defects at 8 and 12 weeks. Histological analysis of experimental group A showed a better Wakitani score (P ＜0.05) than in experimental group B at 8 and 12 weeks after the operation.Conclusions In the repair of full-thickness articular cartilage defects in rabbits, low-energy shock waves in microfracture holes facilitated the production of hyaline-like cartilage repair tissues more than microfracture alone. This model demonstrates a new method of improving microfracture and applying shock waves in vivo. However, longer-term outcomes require further study.