The aim of this study was to further explore the use of magnetic resonance imaging (MRI), magnetic resonance angiography (MRA), and dual-energy X-ray absorptiometry (DEXA) to assess bone formation and blood circulation in a pedicled bone graft substitute. In 14 Wistar rats, initially 10 weeks old, heterogeneous demineralized femur bone matrix implants were wrapped in pedicled adductor thigh muscle flaps. One rat died after surgery. Subsequently, bone formation and maintenance of blood vessel functionality were evaluated in six rats 6 weeks postimplantation by means of in vivo MRI/MRA and postmortem histomorphometry. The other seven rats were left for 12 weeks, whereafter bone formation was evaluated by in vivo DEXA and postmortem histomorphometry. The results demonstrated that after 6 weeks bone formation was present in four of six animals, quantified as 42 (+/-35)% and 25 (+/-19)% by means of MRI and histomorphometry, respectively. MRA was able to show patency of the pedicles of these four rats only, which suggests that the lack of blood supply in the other two rats is the cause of the failure to form bone. In the 12-week group, histology showed increased bone formation without signs of osteolysis, which was quantified histomorphometrically to be as high as 48 (+/-15)%. DEXA failed to show bone formation. It is concluded that in vivo MRI proved to be a reliable method for monitoring ectopic bone formation in a rat model, whereas in vivo DEXA was unable to detect the implants. Furthermore, in vivo MRA proved to be a useful technique for studying the circulation of muscle flaps in this animal model.