Purpose: This study compared the effects of coating implants with hydroxyapatite (HA) using an ion beam-assisted deposition (IBAD) method prepared with machined, anodized, sandblasted and large-grit acid etched (SLA) surfaces in minipigs, and verified the excellency of coating method with HA using IBAD. Material and Methods: 4 male Minipigs(Prestige World Genetics, Korea), 18 to 24 months old and weighing approximately 35 to 40 kg, were chosen. All premolars and first molars of the maxilla were carefully extracted on each side. The implants were placed on the right side after an 8 week healing period. The implant stability was assessed by resonance frequency analysis (RFA) at the time of placement. 40 implants were divided into 5 groups; machined, anodized, anodized plus IBAD, SLA, and SLA plus IBAD surface implants. 4 weeks after implantation on the right side, the same surface implants were placed on the left side. After 4 weeks of healing, the minipigs were sacrificed and the implants were analyzed by RFA, histology and histometric. Results: RFA showed a mean implant stability quotient (ISQ) of $75.625{pm}5.021$, $76.125{pm}3.739$ ISQ and $77.941{pm}2.947$ at placement, after 4 weeks healing and after 8 weeks, respectively. Histological analysis of the implants demonstrated newly formed, compact, mature cortical bone with a nearby marrow spaces. HA coating was not separated from the HA coated implant surfaces using IBAD. In particular, the SLA implants coated with HA using IBAD showed better contact osteogenesis. Statistical and histometric analysis showed no significant differences in the bone to implant contact and bone density among 5 tested surfaces. Conclusion: We can conclude that rough surface implants coated with HA by IBAD are more biocompatible, and clinical, histological, and histometric analysis showed no differences when compared with the other established implant surfaces in normal bone.