Biphasic calcium phosphate (BCP) and poly epsilon-caprolactone (PCL) each have many applications as tissue repair materials. In this study, a three dimensional (3D) PCL infiltrated BCP scaffold was prepared. This composite was further modified and bio-functionalized for bone tissue engineering by subsequent amination and immobilization technique using silicon (Si) and fibronectin (FN) on the surfaces (BCP/PCL+Si and BCP/PCL+Si+FN). In this study, such 3D porous scaffolds were evaluated for bone formation applicability. In vitro studies by immunocytochemistry showed cell morphology and adherence on these scaffolds. Interconnected networks like appearance of tubulin and vinculin expression were notably higher in BCP/PCL+Si and BCP/PCL+Si+FN scaffold surfaces than BCP/PCL surfaces. The scaffolds were also investigated detailed and quantitatively using micro-CT tomography for the repair of bone defects (4 mm diameter) in rats. Micro-CT tomography showed the BCP/PCL+Si+FN scaffolds were almost replaced by newly grown bone within 12 weeks after surgery, suggesting that they have an especially strong capacity for osteogenesis, mineralization, and biodegradation for bone replacement. (C) 2014 Elsevier B.V. All rights reserved.