We present here an overview of the scientific literature concerning the clinical application of autografts and allografts of the skeletal tissues and of the natural and synthetic bone graft substitutes available in small animal orthopedic surgery for resolution of congenital, traumatic and tumoral etiology situations or for reconstructive artroplastic surgeries. This article focuses the terminology, definitions and characteristics of the bone grafts and bone graft substitutes based in their functions and composition, the process of incorporation of the bone grafts and bone graft substitutes, the collection of autogenous cancellous or corticocancellous bone for grafting, the available commercial forms of bone graft or bone graft substitutes and the biologic/synthetic composite grafts, other accessible options in small animal orthopedic surgery with osteogenic and/ or osteoindutive characteristics (ex. collection and use of the autogenous bone marrow or platelet rich plasma), the principal clinical indications and surgical techniques in which are recommended the use of bone graft and/or bone graft substitutes and how to select the best option for each specific clinical case. At last, the future perspectives in reconstructive orthopedic surgery are also pointed, namely the tissue engineering of bone and cartilage tissues and the medical three dimensional biomodulation.