Estrous cycle-related variations of spatial reference memory and neurochemistry in intact female mice were examined. Spatial reference memory was tested in cycling females, ovariectomized (OVX) females, and males by using a 1-day water maze protocol. Choline acetyltransferase (ChAT) and glutamic acid decarboxylase (GAD) activities were measured in the hippocampus and neocortex. Estrus females exhibited worse spatial acquisition and 30-min retention than did proestrus and metestrus females, higher neocortical ChAT activity than proestrus females, and higher neocortical GAD activity than OVX females and males. Neocortical, rather than hippocampal, neurochemistry was more sensitive to hormonal modulation, suggesting that hormonal mediation of neocortical function may play a critical role in regulating spatial reference memory in female mice.