Spontaneous, large scale fluctuations (LSF) in neocortical fMRI activity may result from arousal variations. To investigate the role of arousal, we examined an fMRI database for local fMRI changes at subcortical arousal-regulating structures associated with widespread fMRI co-activations in the neocortex. We identified three subcortical regions that showed anti-polar signal changes with LSF. These regions, known for promoting wakefulness, included the Nucleus Basalis, the Dorsal Midline Thalamus, and the Substantia Nigra. This finding is further evidence of a putative role of arousal in LSF, and suggest that caution should be exercised when extracting functional connectivity measures from fMRI data.