Prepuberal female rats (25 days of age) were injected with estradiol benzoate (EB 10 micrograms/rat, s.c. in oil) or oil vehicle. Forty-eight hours after treatment, all animals were decapitated, their brains removed and sectioned. The arcuate nucleus of the hypothalamus and median eminence were microdissected and processed for isoelectric focusing followed by slab gel electrophoresis. The resulting two-dimensional electrophoretic gels were analyzed to quantitate the specific proteins resolved using a scanning microdensitometric method. Out of 235 proteins measured, 8 proteins were found to be significantly increased and 4 were decreased by EB treatment. The proteins which increased in concentration ranged in molecular weight from 15 to 43 kDa and isoelectric points (pI) of 4.9 to 7.0. The 4 proteins decreased by the EB treatment were 44, 67, 74 and 80 kDa in molecular weight and their pI's ranged from 6.5 to 7.1. It is suggested that these proteins might be involved in some of the neuroendocrine effects that are induced by estradiol in this region of the brain.