The hypothalamic arcuate nucleus integrates different hormonal and neural signals to control neuroendocrine events, feeding, energy balance and reproduction. Previous studies have shown that in adult female rats the arcuate nucleus undergoes a cyclic fluctuation in the number of axo-somatic synapses during the estrous cycle, in parallel to the variation of ovarian hormone levels in plasma. In the present study we have used an unbiased stereological analysis in conjunction with postembedding immunocytochemistry to assess whether the synaptic remodeling during the estrous cycle in rats is specific for certain types of synapses. Our findings indicate that there is a significant decrease in the number of GABAergic axo-somatic synapses on proestrus afternoon and estrus day compared with other days of the estrous cycle. This decrease in GABAergic synapses is accompanied by an increase in the number of dendritic spine synapses. The synaptic density appears to cycle back to proestrus morning values on metestrus day. In contrast, the number of synapses on dendritic shafts does not change during the cycle. These results indicate that a rapid and selective synaptic turnover of arcuate synapses occurs in physiological circumstances.