Spectroscopic methods have been developed to study protein permeation and release kinetics in multi-well plates. The permeation of bovine serum albumin (BSA) through a membrane, which separated a 96-well plate in two compartments, was characterized. A change in fluorescence intensity was measured corresponding to the permeation of BSA from one compartment to another. The permeation of BSA was influenced by the pore size and pore density size of the membrane. The multi-well plates were also used to study the release of a protein drug, hirudin, from an agar hydrogel. A hirudin formulation was mixed at 60 degrees C with liquid agar and the mixture turned to a gel by cooling at room temperature. The gel entrapping hirudin was formed inside the wells of a 96-well plate. On top of the 100microl agar-hirudin gel a volume of 200microl of 10mM phosphate buffer pH 7.4, 140mM NaCl was added. The release kinetics of hirudin from the gel were measured following the changes in the hirudin intrinsic tyrosine fluorescence. The release of hirudin over 12h was measured at three positions: at the bottom of the agar gel, at the interface of the gel with the solution, and in the middle of the receiver solution. The data presented in this paper indicate that high throughput methods can be applied in the characterization of protein drug release from drug delivery systems using small sample volumes.