We present a new method that combines protein-specific fluorescence staining with confocal microscopy to simultaneously measure matrixand surface protein deposits via optical sectioning of hydrogel contact lenses. Tetramethylrhodamine isothiocyanate (TRITC), Texas Red™, fluorescein isothiocyanate (FITC), and fluorescein succinate were used to selectively react with the lysine residues of protein deposits for two lens types (etafilcon A [a 58% water, ionic lens] and polymacon [a 38% water, nonionic lens]). Because TRITC and Texas Red gave high levels of nonspecific staining, they were discontinued. Following exhaustive rinsing of lenses, central lens buttons were analyzed using a Bio-Rad MRC- 500 laser scanning confocal microscope. Optical sections were made every 4 µm at 200x magnification, and the fluorescence signals were processed using image analysis software. The high water ionic material accumulated protein much more rapidly than the low water nonionic material. For a given lens type a correlation was observed between the wear time and the degree of protein deposition; however, we did observe significant inter-subject variations in total protein. From this preliminary work, we conclude that this confocal method is feasible and desirable for simultaneous determination of surface and matrix protein deposition.