The ability to selectively process relevant stimuli is a fundamental function of the primate visual system. The best understood correlate of this function is the enhanced response of neurons in visual cortex to attended stimuli1,2. However, recent results show that the superior colliculus (SC), a midbrain structure, also plays a crucial role in visual attention3–5. It has been assumed that the SC acts through the same well-known mechanisms in visual cortex3,5. Here we tested this hypothesis by transiently inactivating the SC during a motion-change detection task and measuring responses in two visual cortical areas. We found that despite large deficits in visual attention, the enhanced responses of neurons in visual cortex to attended stimuli were unchanged. These results show that the SC contributes to visual attention through mechanisms that are independent of the classic effects in visual cortex, demonstrating that other processes must play a major role in visual attention.