Objective: To investigate the bone response to threaded polyetheretherketone (PEEK) implants coated with nanohydroxyapatite. Materials and methods: A total of 39 PEEK implants were coated with nanocrystalline hydroxyapatite and 39 uncoated implants were used as controls. The implant surface was characterized by optical interferometry and scanning electron microscope. The implants were inserted in the tibia and femur of 13 rabbits. After 6 weeks of healing, quantitative and qualitative analyses were performed. Results: The test implants showed significantly higher removal torque test values compared with the control group. Histomorphometric evaluation demonstrated higher bone-to-implant contact for the test implants; however, there were no differences in bone area between the groups. Qualitative histological analyses demonstrated inflammatory cellular reactions in close vicinity of both implant surfaces. A two-cell layer of foreign body giant cells was observed irrespective of sample type. Conclusion: Our findings demonstrate that implants with a threaded design render good stability to PEEK in both coated and uncoated implants. Nanohydroxyapatite-coated PEEK implants demonstrated improved bone formation compared with uncoated controls.