The concept of tissue and cell guidance is rapidly evolving as more information regarding the effect of the microenvironment on cellular function and tissue morphogenesis become available. These disclosures have lead to a tremendous advancement in the design of a new generation of multifunctional biomaterials able to mimic the molecular regulatory characteristics and the three-dimensional architecture of the native extracellular matrix. Micro- and nano-structured scaffolds able to sequester and deliver in a highly specific manner biomolecular moieties have already been proved to be effective in bone repairing, in guiding functional angiogenesis and in controlling stem cell differentiation. Although these platforms represent a first attempt to mimic the complex temporal and spatial microenvironment presented in vivo, an increased symbiosis of material engineering, drug delivery technology and cell and molecular biology may ultimately lead to biomaterials that encode the necessary signals to guide and control developmental process in tissue- and organ-specific differentiation and morphogenesis.