Understanding the interfacial reactions to synthetic bone regenerative scaffolds in vivo is fundamental for improving osseointegration and osteogenesis. Using transmission electron microscopy, it is possible to study the biological response of hydroxyapatite (HA) and zirconia (ZrO₂) scaffolds at the nanometer scale. Using this technique, the bone-bonding abilities of HA and ZrO₂ scaffolds produced by free form fabrication were evaluated in the human maxilla at 3 and 7-months. A novel focused ion beam (FIB) sample preparation technique enabled the production of thin lamellae for study by scanning transmission electron microscopy (STEM). Interface regions were investigated using high-angle annular dark-field (HAADF) imaging, energy dispersive x-ray spectroscopy (EDXS) analysis and Z-contrast electron tomography. The absence of an interfacial apatite layer in the ZrO₂ samples suggests the formation of a direct contact with bone, while HA bonds through an apatite layer that shows indications of resorption with increasing implantation time. Interfacial apatite layers of 80 and 50nm thickness were noted in the 3 and 7-month HA samples, respectively and bone growth was discovered in micropores up to 10μm into the samples. Viewing this structure in three dimensions enabled us to observe the nanometer differences in orientation of hydroxyapatite crystals in the collagen matrix of the bone and crystals precipitated on the implant surface. This study demonstrates the potential of hydroxyapatite and zirconia scaffolds for use as bone regenerative materials.