Scaffolds made of polycaprolactone and nanocrystalline silicon-substituted hydroxyapatite have been fabricated by 3D printing rapid prototyping technique. To asses that the scaffolds fulfill the requirements to be considered for bone grafting applications, they were implanted in New Zealand rabbits. Histological and radiological studies have demonstrated that the scaffolds implanted in bone exhibited an excellent osteointegration without the interposition of fibrous tissue between bone and implants and without immune response after 4 months of implantation. In addition, we have evaluated the possibility of improving the scaffolds efficiency by incorporating demineralized bone matrix during the preparation by 3D printing. When demineralized bone matrix (DBM) is incorporated, the efficacy of the scaffolds is enhanced, as new bone formation occurs not only in the peripheral portions of the scaffolds but also within its pores after 4 months of implantation. This enhanced performance can be explained in terms of the osteoinductive properties of the DBM in the scaffolds, which have been assessed through the new bone tissue formation when the scaffolds are ectopically implanted.