In spite of many researches on scaffold material design, fabrication and characterization, as well as cell-material interaction in vitro, in vivo study especially in large mammals should be an essential step towards practical application. In our center, different scaffold materials have been applied to the reconstruction of various types of tissues using immunocompetent mammals as major animal models, such as for reconstruction of bone, cartilage, tendon, skin, blood vessel and corneal stroma, etc. In this article, our experience, as well as encountered challenges in the application of scaffold materials, is introduced. Additionally, future requirements for scaffold application in tissue reconstruction and regeneration are proposed as well.