Inflammation-related molecules, thought to be derived from microglia, are involved in behavioral changes induced by repeated stress. Indeed repeated stress induces morphological changes of microglia. However, the nature of microglial response to repeated stress and its molecular mechanism remain unknown. Since innate immune molecules including Toll-like receptors (TLRs) are known to regulate microglia, we examined a role for TLRs in repeated social defeat stress, and found that mice deficient in TLRs and MyD88, their adaptor signaling molecule, fail to show social avoidance and elevated anxiety induced by repeated stress. However, these knockout mice showed normal increase in submissive posture with repetition of stress, suggesting a role for TLR-MyD88 pathway in a specific subset of stress-induced behavioral changes. Since the medial prefrontal cortex (mPFC) is critical for stress-induced behavioral changes, we examined stress-induced responses in mPFC neurons using c-Fos immunoreactivity. In wild-type mice, single defeat stress increased the number of c-Fos-positive neurons in the mPFC, and this stress response was attenuated with repetition of stress. TLR deficiency partially reduced repeated stress-induced attenuation of c-Fos response. Consistent with a role for microglia, mRNA expression of pertinent TLR isoforms and MyD88 was detected in microglia isolated from adult mice, and repeated stress induced morphological changes in microglia in the mPFC in a TLR-dependent manner. These data demonstrate a critical role for innate immune signaling in behavioral, neuronal and microglial changes induced by repeated stress, and pave the way for elucidating a role for neuron-microglia interaction in stress-induced behavioral changes.