In the tissue engineering field, the design of the scaffold inspired on the natural occurring tissue is of vital importance. Ideally, the scaffold surface must promote cell growth and differentiation, while promote angiogenesis in the in vivo implant of the scaffold. On the other hand, the material selection must be biocompatible and the degradation times should meet tissue reparation times. In the present work, we developed a nanofibrous scaffold based on chitosan crosslinked with diisopropylfumarate-vinyl acetate copolymer using anodized aluminum oxide (AAO) templates. We have previously demonstrated its biocompatibility properties with low cytotoxicity and proper degradation times. Now, we extended our studies to demonstrate that it can be successfully nanostructured using the AAO templates methodology, obtaining a nanorod-like scaffold with a diameter comparable to those of collagen fibers of the bone matrix (170 and 300 nm). The nanorods obtained presented a very homogeneous pattern in diameter and length, and supports cell attachment and growth. We also found that both osteoblastic and chondroblastic matrix production were promoted on bone marrow progenitor cells and primary condrocytes growing on the scaffolds, respectively. In addition, the nanostructured scaffold presented no cytotoxicity as it was evaluated using a model of macrophages on culture.