In the present study, the effects of implant design and surface properties on peri-implant bone response were evaluated with both conventional histomorphometry and micro-computed tomography (micro-CT), using two geometrically different dental implants (Screw type, St; Push-in, Pi) either or not surface-modified (non-coated, CaP-coated, or CaP-coated+TGF-beta1). After 12 weeks of implantation in a goat femoral condyle model, peri-implant bone response was evaluated in three different zones (inner: 0-500 microm; middle: 500-1000 microm; and outer: 1000-1500 microm) around the implant. Results indicated superiority of conventional histomorphometry over micro-CT, as the latter is hampered by deficits in the discrimination at the implant/tissue interface. Beyond this interface, both analysis techniques can be regarded as complementary. Histomorphometrical analysis showed an overall higher bone volume around St compared to Pi implants, but no effects of surface modification were observed. St implants showed lowest bone volumes in the outer zone, whereas inner zones were lowest for Pi implants. These results implicate that for Pi implants bone formation started from two different directions (contact- and distance osteogenesis). For St implants it was concluded that undersized implantation technique and loosening of bone fragments compress the zones for contact and distant osteogenesis, thereby improving bone volume at the interface significantly.