Adult dendritic arbors and spines can be modulated by environment and gonadal hormones that have been reported to affect also those of hippocampal and prefrontal cortical neurons. Here we investigated whether female gonadal hormones and estrous cycle alter the dendrites of primary cortical neurons. We employed intracellular dye injection in semifixed brain slices and 3-dimensional reconstruction to study the dendritic arbors and spines of the major cortical output cells, layer III and V pyramidal neurons, during different stages of the estrous cycle. Dendritic spines of both pyramidal neurons were more numerous during proestrus than estrus and diestrus, whereas dendritic arbors remained unaffected. Ovariohysterectomy (OHE) reduced dendritic spines by 24-30% in 2 weeks, whereas subcutaneous estrogen or progesterone supplement restored it to normal estrous/diestrous level in 14 days; neither treatment affected the dendritic arbors. Reduction of dendritic spines following OHE was associated with decrease of PSD-95 suggesting decrease of excitatory synapses. Thus, fluctuation of gonadal hormones during the female sex cycle is likely to modulate primary cortical functions and loss of gonadal hormones for instance following menopause might compromise cortical function, and the effect could be reversed by exogenous female sex hormones.