The aim of this study is to evaluate the effects of coating implants with hydroxyapatite (HA) by an ion beam-assisted deposition (IBAD) method and to compare them with implants prepared with machined and anodized surfaces. Twenty-four implants in this study were divided into three groups; machined, anodized, anodized plus IBAD surface implants. Implant stability and osseointegration were assessed by resonance frequency analysis (RFA) and histologic analysis. We can conclude that implants coated by HA by IBAD demonstrate characteristics of contact osteogenesis, but the research design does not permit conclusions regarding long-term treatment outcome with implants. Further studies are needed.