Synesthesia is a condition where stimulation of a single sensory modality or processing stream elicits an idiosyncratic, yet reliable perception in one or more other modalities or streams. Various models have been proposed to explain synesthesia, which have in common aberrant cross-activation of one cortical area by another. This has been observed directly in cases of linguistic-color synesthesia as cross-activation of the 'color area', V4, by stimulation of the grapheme area. The underlying neural substrates that mediate cross-activations in synesthesia are not well understood, however. In addition, the overall integrity of the visual system has never been assessed and it is not known whether wider differences in sensory-perceptual processing are associated with the condition. To assess whether fundamental differences in perceptual processing exist in synesthesia, we utilised high-density 128-channel electroencephalography (EEG) to measure sensory-perceptual processing using stimuli that differentially bias activation of the magnocellular and parvocellular pathways of the visual system. High and low spatial frequency gratings and luminance-contrast squares were presented to 15 synesthetes and 15 controls. We report, for the first time, early sensory-perceptual differences in synesthetes relative to non-synesthete controls in response to simple stimuli that do not elicit synesthetic color experiences. The differences are manifested in the early sensory components of the visual evoked potential (VEP) to stimuli that bias both magnocellular and parvocellular responses, but are opposite in direction, suggesting a differential effect on these two pathways. We discuss our results with reference to widespread connectivity differences as a broader phenotype of synesthesia.