Objective To compare the healing quality of bone to bone and bone to tendon repair in a patella-patellar tendon complex. Methods A standard transverse osteotomy was performed at the distal one-third of patella of one hindlimb of 60 mature female rabbits. Both patellar fragments were reattached for bone to bone group while the patellar tendon was reattached to the remaining patella after removing the distal one-third of patella for bone to tendon group. Patella-patellar tendon complex was harvested at 8, 12 and 24 weeks post-operatively for biomechanical and histological evaluations. Results No significant differences in the failure loads were found between two groups. However, greater ultimate stress was found in bone to bone group as compared with bone to tendon group at week 8 and 24 (both P<0.05). Histology revealed that the bone to bone healing was via endochondral ossification at the healing interface. In bone to tendon group, extensive scar tissue was formed to overbridge the healing interface and remodeled with healing over time. The structural integration at the tendon and bony healing interface was poor and no typical intermitted fibrocartilage zone as seen in normal bone to tendon junction was formed. Conclusion The findings of this study may suggest that the anatomical reconstruction of patella-patellar tendon complex injury may be the primary concern in decision making for selecting either bone to bone or bone to tendon repair. However whenever possible, to initial fracture (bone-to-bone) fixation for ensuring better and predictable repair at the healing interface.