The role of the material composition, porosity and surface topography of scaffolds for promotion of osteogenesis and osseointegration is not fully understood. The aim of the present study was to evaluate the effects of material composition and surface topography on bone ingrowth and bone contact. Designed macroporous ceramic scaffolds of zirconia and hydroxyapatite were used. Using free form fabrication (FFF) techniques an identical macroporosity in both materials was achieved. The scaffolds were implanted in rabbit tibia (cortical bone) and femur (trabecular bone). After 6 weeks of implantation the tissue response was assessed with histology and histomorphometry. The results showed significantly more bone ingrowth and bone contact in the hydroxyapatite scaffolds compared to the zirconia scaffold. Surface topography had no significant effect on bone contact inside the macropores regardless of material. This was observed in both cortical and trabecular bone sites. The study suggests that the difference between hydroxyapatite and zirconia was due to a difference in material chemistry.