Scaffolds play a pivotal role in the tissue engineering paradigm by providing temporary structural support, guiding cells to grow, assisting the transport of essential nutrients and waste products, and facilitating the formation of functional tissues and organs. Single-walled carbon nanotubes (SWNTs), especially ultra-short SWNTs (US-tubes), have proven useful for reinforcing synthetic polymeric scaffold materials. In this article, we report on the in vivo biocompatibility of US-tube reinforced porous biodegradable scaffolds in a rabbit model. US-tube nanocomposite scaffolds and control polymer scaffolds were implanted in rabbit femoral condyles and in subcutaneous pockets. The hard and soft tissue response was analyzed with micro-computed tomography (micro CT), histology, and histomorphometry at 4 and 12 weeks after implantation. The porous US-tube nanocomposite scaffolds exhibited favorable hard and soft tissue responses at both time points. At 12 weeks, a three-fold greater bone tissue ingrowth was seen in defects containing US-tube nanocomposite scaffolds compared to control polymer scaffolds. Additionally, the 12 week samples showed reduced inflammatory cell density and increased connective tissue organization. No significant quantitative difference in polymer degradation was observed among the various groups; qualitative differences between the two time points were consistent with expected degradation due to the progression of time. Although no conclusions can be drawn from the present study concerning the osteoinductivity of US-tube nanocomposite scaffolds, the results suggest that the presence of US-tubes may render nanocomposite scaffolds bioactive assisting osteogenesis.