A basic approach toward the design of three-dimensional (3D) rapid prototyped magnetic scaffolds for hard-tissue regeneration has been proposed. In particular, 3D scaffolds consisting of a poly(ε-caprolactone) (PCL) matrix and iron oxide (Fe3O4) or iron-doped hydroxyapatite (FeHA) nanoparticles were fabricated through a 3D fibre deposition technique. As a first approach, a polymer to nanoparticle weight ratio of 90/10 (wt/wt) was used. The effect of the inclusion of both kinds of nanoparticles on the mechanical, magnetic, and biological performances of the scaffolds was studied. The inclusion of Fe3O4 and FeHA nanoparticles generally improves the modulus and the yield stress of the fibres if compared to those of neat PCL, as well as the modulus of the scaffolds. Micro-computed tomography has confirmed the possibility to design morphologically-controlled structures with a fully interconnected pore network. Magnetisation analyses performed at 37°C have highlighted M-H curves that are not hysteretic; values of saturation magnetisation (Ms) of about 3.9 emu/g and 0.2 emu/g have been evaluated for PCL/Fe3O4 and PCL/FeHA scaffolds, respectively. Furthermore, results from confocal laser scanning microscopy (CLSM) carried out on cell-scaffold constructs have evidenced that human mesenchymal stem cells (hMSCs) better adhered and were well spread on the PCL/Fe3O4 and PCL/FeHA nanocomposite scaffolds in comparison with the PCL structures.