Objective: To evaluate the biological effects of three calcium phosphate (CaP) coatings with nanostructures on relatively smooth implant surfaces. Material and methods: Stable CaP nanoparticle suspensions of different particle sizes and structures were coated onto implants by immersion and subsequent heat treatment. An uncoated implant was used as the control. After topographical and chemical characterizations, implants were randomly inserted into rabbit tibiae for removal torque (RTQ) testing. To confirm the biological reaction, implants were placed in the bilateral femurs of three rabbits. Results: The topographical characterization showed that each surface had different nanostructural characteristics and X-ray photon spectroscopy showed various CaP compositions. The control and test groups had different nanotopographies; however, the differences among the test groups were only significant for Surfaces B and C and the rest were insignificant. The RTQ tests showed significantly higher values in two test groups (Surface A and Surface C). Histologically, no adverse effects were seen in any group. Histomorphometrical evaluation showed comparable or better osseointegration along the implant threads in the test groups. Conclusion: The three different CaP coatings with nanostructures on the implant surfaces had enhancing effects on osseointegration. Along with the surface nanotopography, the CaP chemistry might have influenced the biological outcomes.