Ongoing activity is ubiquitous in the cortex and recently has been implied to play a significant functional role in shaping sensory-evoked responses by reflecting the momentary internal state of the brain together with its knowledge about the external world (Berkes et al., Science 2011). A wide variety of studies also reported that ongoing neural signal variability in many cortical areas gets reduced when a stimulus is presented (Churchland et al., Nat Neuro 2010), raising the possibility that this reduction is functionally linked to the decrease of uncertainty due to the stimulus onset (Orban et al., Cosyne 2011). This conjecture would imply that just as stimulus onset reduces uncertainty and hence neural response variability, ongoing signal variability should also decrease due to reduction of uncertainty when the animal can apply acquired long-term knowledge about the environment in a particular situation. To test this hypothesis, we recorded neural activity with multi-electrode arrays simultaneously from the primary visual and gustatory cortices of rats while they learned to associate visual cues with delayed water reinforcement. We found within-modality, cue-dependent suppression of variability of the evoked activity in the visual cortex in line with previous reports. However, we also found that, independent of firing rate changes, spike count variability in the absence of any sensory stimuli was significantly suppressed both during the delay periods in the primary visual cortex, and during the cue period in the ongoing activity of the gustatory cortex. Importantly, this suppression both within and across modalities occurred only in animals that learned the task. These findings demonstrate that not only domain-specific stimulus-evoked, but also experience-based, internally-generated cross-modal signals are capable of suppressing the variability of ongoing activity in the primary cortex supporting the proposal that this activity is not noise but rather it represents information about particular behaviorally-relevant conditions.