Clinicians have made practical efforts for over 100 years in replacing damaged tissues and organs. However, organ shortage and rejection still remain major challenges. Rapidly emerging tissue engineering, which is interdisciplinary medical science and technology, has gained attention to resolve the challenges. The grand aim of tissue engineering is to develop implantable tissue constructs via in vitro culture of cells seeded in three-dimensional (3-D) scaffolds formed in biomaterials. Microengineering and microfluidic techniques have demonstrated promising proof-ofconcept in developing potentially valuable in vitro culture systems. However, in conventional microfluidic systems, the culture environment is confined to channels. Moreover, most of currently existing cell culture systems do not allow for the creation of fully functional tissues. This limitation is also due to a lack of understanding principles of tissue function and growth. Tissue-scale biology, combined with molecular and cell biology, would allow for better understandings of the principles, and can be complementarily interconnected to tissue engineering. Therefore, we must develop in vitro tools to overcome the challenges and to enable tissue engineering and tissue-scale biology. The development of the enabling tools could lead to exploitation of detailed principles and mechanisms in the study of physiological and pathological processes in a quantitative manner. First, we present the development of microfluidic scaffolds that are formed by embedding microfluidic networks directly within biomaterials. Experiments with chondrocytes in calcium alginate demonstrated that these embedded microchannels enable the maintenance of a uniform metabolic environment within the bulk of the scaffold and the creation of distinct soluble environments experienced by cells in their 3-D environment. The generalization of the process into type I collagen allows for the embedded microchannels to serve as a template for microvascular endothelialization within a matrix that can support cellular remodeling. In the new experimental context offered by these microfluidic scaffolds, we present detailed mass transport considerations in microfluidic biomaterials. Such considerations include quantitative measurements of 1) diffusion of non-reactive solutes and 2) metabolic activity of reactive solutes such as oxygen, which should be also used in designing and operating microfluidic biomaterials. Finally, we present the development of oxygen-sensing particles that are dispersible in aqueous environment and biocompatible. Experiments show that the oxygen-sensing particles also allow monitoring oxygen concentration in a both spatially and temporally resolved manner. We can use this tool for the direct visualization and optical measurement of oxygen-depletion lengths within cell-seeded 3-D scaffolds in vitro, and the measurement of oxygen levels in animal blood streams in vivo.