Stereopsis is critical for interaction with our environment. However, binocular disparity in natural images is often ambiguous and this makes it difficult to establish a binocular correspondence solution. In my thesis, I focus on both the challenges of this problem and solutions that the brain applies. To study brain function, I use Transcranial Magnetic Stimulation (TMS) which allows me to causally relate induced changes in neural activity with changes in depth perception. This way I can map out neural mechanisms of stereopsis within the visual cortex. As a first step, I conducted a proof of concept study to confirm where in the visual cortex TMS can be used to study perception. I systematically mapped out where in the visual cortex TMS triggers self-propagating, perceptually noticeable neural activation. I related this to the retinotopic organisation and the location of object- and motion-selective areas, identified by functional Magnetic Resonance Imaging. My work confirms that TMS can trigger perceptually significant neural activation in early and dorsal visual areas. In my second chapter, I investigated how incoherent binocular disparity challenges stereopsis. As disparity coherence is reduced it becomes increasingly challenging to establish global correspondence and consequently observers struggle to perceive depth. Interestingly, this problem is less severe when images contain a mixture of bright and dark features (mixed contrast polarity). By locating where in the brain disparity processing benefits from mixed contrast polarity, I can infer where incoherent disparity might challenge mechanisms of stereopsis. I applied TMS during discrimination of incoherent disparity in images with mixed or single contrast polarity. I found that stimulation over V1 differentially affects perception of mixed and single polarity stimuli. My findings show that mechanisms of stereopsis in early visual cortex process mixed and single polarity differently and suggest these mechanisms are challenged by incoherent disparity. In my final chapter, I investigated the role of parietal cortex in the processing of incoherent disparity information. Findings in both macaque monkeys and human observers suggest that the dorsal visual cortex is particularly involved in the processing of incoherent disparity signals. Here, I tested the role of the posterior parietal cortex in human observers. I used brain stimulation to suppress synaptic transmission in parietal cortex and recorded electroencephalography during incoherent disparity processing. Disrupting parietal cortex caused changes in early, disparity responses in visual cortex. This suggests that parietal cortex provides top-down influence to the visual cortex relevant to incoherent disparity processing.