Here, we report the preparation of hydroxyapatite nanotubes for specific use as bone regeneration material. The nanofiber mesh of a polymer (polycaprolactone) used as a template was mineralized within solutions via a biomimetic process. A subsequent heat-treatment (over 500°C) completely eliminated the inner polymer, resulting in preserving the surface mineral phase in the form of nanotubes. The nanotubes had diameters of hundreds of nanometers with nonwoven mesh, replicating the initial nanofiber template. Furthermore, the nanotubes revealed a phase of poorly crystallized apatite, mimicking biological bone mineral. The developed biomimetic apatite nanotubes may be useful for bone regeneration as a new type of biomaterial.