In this chapter, we describe the fundamental aspects of the preparation of molecularly-defined scaffolds for soft tissue engineering, including the tissue response to the scaffolds after implantation. In particular, scaffolds prepared from insoluble type I collagen fibres, soluble type II collagen fibres, insoluble elastin fibres, glycosaminoglycans (GAGs) and growth factors are discussed. The general strategy is to prepare tailor-made "smart" biomaterials which will create a specific microenvironment thus enabling cells to generate new tissues. As an initial step, all biomolecules used were purified to homogeneity. Next, porous scaffolds were prepared using freezing and lyophilisation, and these scaffolds were crosslinked using carbodiimides. Crosslinking resulted in mechanically stronger scaffolds and allowed the covalent incorporation of GAGs. Scaffold characteristics were controlled to prepare tailor-made scaffolds by varying e.g. collagen to elastin ratio, freezing rate, degree of crosslinking, and GAGs attachment. The tissue response to scaffolds was evaluated following subcutaneous implantations in rats. Crosslinked scaffolds maintained their integrity and supported the formation of new extracellular matrix. Collagen-GAG scaffolds loaded with basic fibroblast growth factor significantly enhanced neovascularisation and tissue remodelling. Animal studies of two potential applications of these scaffolds were discussed in more detail, i.e. for bladder and cartilage regeneration.