Recently the fabrication of 3D scaffolds with the potential of application as flexible bone graft substitutes has been attracted many researches. In this research, a 3D nanocomposite scaffold composed of gelatin and hydroxyapatite was proposed by employing the freeze-drying methods. Nanoparticles of Fe3O4 were added to the gelatin/hydroxyapatite in order to magnetize the 3D nanocomposite scaffold. Addition of magnetite particles makes the 3D nanocomposites an appropriate drug carrier, which can trigger drug release by an external magnetic field stimulation. Therefore, the scaffold can play the role of bone substitute and drug carrier simultaneously. The microstructure and morphology of these scaffolds were investigated using Fourier transform infrared spectroscopy (FTIR), X-ray diffraction analysis (XRD), scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS). Elastic modulus and compressive strength of the scaffolds were investigated by a tensile test instrument. The magnetization variation of the scaffolds was investigated by a vibrating sample magnetometer at room temperature. Water and phosphate buffer saline (PBS) solution were utilized to determine the in vitro swelling behavior of the scaffolds after 24 h. The MTT assays on L929 cells was used to study the cytotoxicity of the prepared samples. According to the results, the FTIR spectrum confirms the presence of gelatin, hydroxyapatite and magnetite nanoparticles. The XRD patterns show the presence of ceramic crystalline area in the gelatin/hydroxyapatite network and also the Fe3O4 nanoparticles. SEM images of the scaffolds show a highly interconnected porous structure with maximum 85% porosity. The pore size range of the scaffolds is 120-210 mu m. The SEM-EDS analyses confirms the presence of Fe element in the structure of composites. Comparing the mechanical properties of the scaffolds with the trabecular bone tissue revealed that the compressive strength of the scaffolds is in the adequate range of 2-4.5 MPa. In addition, the magnetization test revealed that the Fe-4 sample with highest amount of Fe3O4 possess a proper magnetic property. Results suggested that by increasing the percentage of Fe3O4 the swelling of sample decreased for both water and PBS solutions. Cell culture experiments exhibited that the scaffold extracts were not cytotoxic in any concentrations. According to the results, the synthesized 3D nanocomposite scaffolds possess a great potential to be used as bone substitute and drug carrier simultaneously. (C) 2017 Elsevier B.V. All rights reserved.