Technology originally developed for the electronics industry is now being adapted for use in miniaturized chemical and biochemical analysis systems. In these lab-on-a-chip, controlled flow of small volumes of fluid through microscopic channels allows for complex, integrated control over chemical assays in a small, inexpensive (often disposable) package. We are currently developing a system that combines microfluidics and single molecule fluorescence detection. The use of a microfluidic device provides precise control over the fluid environment solvating the fluorophores under study. Having this control opens up a wide range of new experiments aimed at understanding molecular dynamics and photophysics on a single molecule level. For example, one application we are working toward is to study individual proteins as they are alternately folded and unfolded by exchanging buffers and monitoring changes in the efficiency of fluorescence resonance energy transfer between two attached fluorophores. Other applications include measuring the heterogeneity in binding constants for enzymes and antibodies, the study of fluorophore solvent shifts and quenching on a molecule-by-molecule basis, the dependence of adsorption/desorption dynamics on solvent compositions, and rotational dynamics of molecules in solvent swelled polymers.