We have recently shown that intrinsic fluctuations of ongoing activity during baseline have an impact on perceptual decisions reported for an ambiguous visual stimulus (Hesselmann et al., 2008). To test whether this result generalizes from the visual object domain to other perceptual and neural systems, the current study investigated the effect of ongoing signal fluctuations in motion-sensitive brain regions on the perception of coherent visual motion. We determined motion coherence thresholds individually for each subject using a dynamic random dot display. During functional magnetic resonance imaging (fMRI), brief events of subliminal, supraliminal, and periliminal coherent motion were presented with long and variable interstimulus intervals between them. On each trial, subjects reported whether they had perceived "coherent" or "random" motion, and fMRI signal time courses were analyzed separately as a function of stimulus and percept type. In the right motion-sensitive occipito-temporal cortex (hMT+), coherent percepts of periliminal stimuli yielded a larger stimulus-evoked response than random percepts. Prestimulus baseline activity in this region was also significantly higher in these coherent trials than in random trials. As in our previous study, however, the relation between ongoing and evoked activity was not additive but interacted with perceptual outcome. Our data thus suggest that endogenous fluctuations in baseline activity have a generic effect on subsequent perceptual decisions. Although mainstream analytical techniques used in functional neuroimaging do not capture this nonadditive effect of baseline on evoked response, it is in accord with postulates from theoretical frameworks as, for instance, predictive coding.