The aim of this study was to assess the osseointegration of two series of titanium (Ti) scaffolds with 0.8 and 1 mm cell size obtained by Selective Laser Melting (SLM) technique. One of the series had the Ti surface unmodified, while the other had the Ti surface coated with silicon-substituted nano-hydroxyapatite (nano-HapSi). The scaffolds were implanted in the femur bone defects of 6 White Californian male rabbits: three animals were implanted with 0.8 mm cell size scaffolds and three animals with 1 mm cell size scaffolds, respectively. The bone fragments and scaffolds harvested at 2, 4 and 6 months were histologically analyzed using conventional light microscopy (LM) and scanning electron microscopy (SEM) for the qualitative evaluation of the bone tissue formed in contact with the scaffold. Both LM and SEM images indicated a better osseointegration for nano-HapSi coated Ti scaffolds. LM revealed that the compact bone formed in the proximity of nano-HapSi-coated scaffolds was better organized than spongy bone associated with unmodified scaffolds. Moreover, Ti scaffolds with meshes of 0.8 mm showed higher osseointegration compared with 1 mm. SEM images at 6 months revealed that the bone developed not only in contact with the scaffolds, but also proliferated inside the meshes. Nano-HapSi-coated Ti implants with 0.8 mm meshes were completely covered and filled with new bone. Ti scaffolds osseointegration depended on the mesh size and the surface properties. Due to the biocompatibility and favorable osseointegration in bone defects, nano-HapSi-coated Ti scaffolds could be useful for anatomical reconstructions.