Fluorescence immunohistochemistry has traditionally been difficult or impossible to perform on the vertebrate lens because of its extremely high protein content. Described here is a robust and rapid method for preparing and labeling vertebrate eyes for confocal microscopy. This technique has successfully been applied to localize proteins in the lens epithelium and capsule, as well as the primary and secondary fibers. This technique preserves tissue morphology and coupled with double and triple labeling, has allowed localization of proteins bound to plasma membrane, basement membrane, nucleus, endoplasmic reticulum as well as sub-nuclear compartments. In addition, the present technique has proven useful for fluorescent immunohistochemical analysis of diverse tissues including whole embryos, adult muscle, pancreas, and liver. This procedure allowed us to successfully localize a wide variety of antigens on diverse vertebrate tissues including the more challenging vertebrate lens.