Frontal eye fields (FEF) and anterior intraparietal sulcus (aIPS) are involved in the control of voluntary attention in humans, but their functional differences remain poorly understood. We examined the activity in these brain regions as a function of task-irrelevant changes in target and nontarget perceptual salience during a sustained spatial attention task. Both aIPS and FEF were engaged during selective attention. FEF, but not aIPS, was sensitive to the direction of spatial attention. Conversely, aIPS, but not FEF, was modulated by the relative perceptual salience of the target and nontarget stimuli. These results demonstrate separable roles for FEF and aIPS in attentional control with FEF more involved in goal-directed spatial attention and aIPS relatively more sensitive to bottom-up attentional influences driven by stimulus salience.