Research to date has focused on the effect of cTBS on the target area, but less is known about its effects on the resting state functional connectivity between different brain regions. We investigated this issue by applying cTBS to the occipital cortex and probing its influence in retinotopically defined regions in early visual cortex using functional MRI. We found that occipital cTBS reliably decreased the resting state functional connectivity (i.e., the correlation of spontaneous activity) between regions of the early visual cortex. In the context of a perceptual task, such an effect could mean that cTBS affects the strength of the perceptual signal, its variability, or both. We investigated this issue in a second experiment in which subjects performed a perceptual discrimination task and indicated their level of certainty on each trial. The results showed that occipital cTBS decreased both subjects' accuracy and confidence. Signal detection modeling suggested that these impairments resulted primarily from a decreased strength of the perceptual signal, with a nonsignificant trend of a decrease in signal variability. We discuss the implications of these experiments for understanding the mechanisms by which cTBS influences brain activity and perceptual processes. cTBS; fMRI; visual cortex; perception; resting state connectivity; signal detection theory REPETITIVE TRANSCRANIAL MAGNETIC stimulation is a popular technique used to transiently affect neural activity in a noninvasive manner. One recently developed variant of repetitive transcranial magnetic stimulation (TMS), continuous theta burst stimulation (cTBS;Huang et al. 2005), has shown promise because of its rapid application (Ͻ1 min), its ability to produce behavioral effects for up to 1 h after stimulation, and its connection to known neuronal mechanisms, such as long-term potentiation and depression (LTD). Indeed, research has shown that cTBS reduces motor cortical excitability in a manner consistent with LTD effects (Allen et al. 2007;Di Lazzaro et al. 2005Gentner et al. 2008;Huang et al. 2005Huang et al. , 2007.When applied to the occipital cortex, cTBS has been found to increase phosphene thresholds (PTs), such that higher stimulation intensity is needed to produce conscious visual experience (Franca et al. 2006). One possibility is that such an increase in PTs is, at least in part, due to decreased connectivity between areas in the early visual cortex, which would make the Here we tested for this possibility by investigating the resting state connectivity between retinotopically defined regions in the early visual cortex after occipital application of cTBS. We identified areas V1, V2, and V3 as three separate regions of interest (ROIs) and found that cTBS decreased the resting state functional connectivity between each pair of regions. In separate analyses, we separated the left and right hemisphere of each of these areas and observed that cTBS decreased the inter-and intrahemispheric resting state connectivity between these retinotopically defined re...