Synthetic materials mimicking the internal porous structure of natural dentin were prepared as nanohybrid matrix scaffolds made of poly(ethyl methacrylate-co-hydroxyethyl acrylate), pure and with a sol-gel-derived interpenetrated silica nanophase, with aligned tubular pores in the micrometer range typical of dentinal tissue. Some of them were internally coated with a layer of hydroxyapatite by immersion in simulated body fluid. Their physicochemical and mechanical properties were investigated. The different types of scaffolds were implanted subcutaneously into immunocompromised nude mice for 4, 6, and 8 weeks and their biological response were analyzed. Optical microscopy was employed to study the scaffold structure and neovascularization. Cells origin, inflammation, and macrophagic responses were evaluated by optical microscopy, immunohistochemistry, and transmission electron microscopy. The scaffold ultrastructural pattern imitates dentinal histological structure. The materials allowed cell colonization and neoangiogenesis. These biomaterials were colonized by murine cells fenotypically different to those of dermal connective tissue, showing structural differentiations. Colonization and viability were improved by the use of mineralized interphases, which showed a cellular distribution resembling a neodentinal pattern. Invasion of the scaffold tubules by single odontoblast-like processes was ascertained both in the noncoated and coated scaffolds. Such materials thus seem promising in tissue engineering strategies for dentin regeneration.