Only a small fraction of all the information reaching our senses can be the object of conscious report or voluntary action. Although some models propose that different attentional states (top-down amplification and vigilance) are necessary for conscious perception, few studies have explored how the brain activations associated with different attentional systems (such as top-down orienting and phasic alerting) lead to conscious perception of subsequent visual stimulation. The aim of the present study was to investigate the neural mechanisms associated with endogenous spatial attention and phasic alertness, and their interaction with the conscious perception of near-threshold stimuli. The only region demonstrating a neural interaction between endogenous attention and conscious perception was the thalamus, while a larger network of cortical and subcortical brain activations, typically associated with phasic alerting, was highly correlated with participants' conscious reports. Activation of the anterior cingulate cortex, supplementary motor area, frontal eye fields, thalamus, and caudate nucleus was related to perceptual consciousness. These data suggest that not all attentional systems are equally effective in enhancing conscious perception, highlighting the importance of thalamo-cortical circuits on the interactions between alerting and consciousness.