Polyether ether ketone (PEEK) possesses excellent mechanical properties similar to those of human bone and is considered the best alternative material other than titanium for orthopedic spine and trauma implants. However, the deficient osteogenic properties and the bioinertness of PEEK limit its fields of application. The aim of this study was to limit these drawbacks by coating the surface of PEEK with nano-scaled hydroxyapatite (HA) minerals. In the study, the biological response to PEEK, with and without HA coating, was investigated. Twenty-four screw-like and apically perforated implants in the rabbit femur were histologically evaluated at 3 weeks and 12 weeks after surgery. Twelve of the 24 implants were HA coated (test), and the remaining 12 served as uncoated PEEK controls. At 3 weeks and 12 weeks, the mean bone–implant contact was higher for test compared to control (
P
<0.05). The bone area inside the threads was comparable in the two groups, but the perforating hole showed more bone area for the HA-coated implants at both healing points (
P
<0.01). With these results, we conclude that nano-sized HA coating on PEEK implants significantly improved the osteogenic properties, and in a clinical situation this material composition may serve as an implant where a rapid bone fusion is essential.