In this study, hydroxyapatite (HAp) obtained by hydrothermal synthesis from natural sources (whelk shells of Rapana thomasiana) was compared to synthetic hydroxyapatite (prepared from chemical reagents) and used for 3D printing of HAp-based structures. Rapana thomasiana can be found in Romanian coast of Black Sea. The visceral part of Rapana is used for culinary purposes, but the whelk shell, mainly consisting of CaCO3, remains as biowaste and can be used as a source of Ca for hydroxyapatite synthesis. Synthetic and natural hydroxyapatite nanopowders were characterized by X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), dynamic light scattering (DLS) method and in vitro tests. XRD and FT-IR have confirmed the formation of nanostructured hydroxyapatite irrespective of the raw material used. Both types of powders were further used for 3D printing of HAp-based structures, which have also been characterized by SEM and in vitro tests. In vitro tests performed on natural HAp disks (made from whelk shell) lack cytotoxicity and were associated with cell viability similar to that for the synthetic hydroxyapatite disk.