To better compare possible changes in soluble protein content during human cataractogenesis, microdissected sections from opaque and highly pigmented versus transparent parts of the lens were analyzed by high pressure liquid chromatography, isoelectric focusing, sodium dodecylsul-fate polyacrylamide gel electrophoresis, and tryptic mapping of radioiodinated peptides. Using this methodology, resolution of proteins and their tryptic peptides can be obtained from individual lens sections containing as little as 5–10μg of protein. Furthermore, the origin of each protein analyzed by these methods can be verified by comparison with tryptic peptide maps of previously purified human crystallins. Included are examples of how this technique can be used to characterize differences in protein composition from opaque versus transparent sections from different human lenses, as well as brunescent vs lightly-pigmented sections from the same human lens.