Eye-tracking which includes the measurements of eye position and pupil size is a popular tool in basic and clinical investigation, because eye movements and pupil size are modulated by various sensory, cognitive, and affective processes. Our recent research has shown similar modulations by bottom-saliency, cognitive, and arousal processes between saccadic and pupillary responses, arguing that the superior colliculus, a midbrain structure causally linked to eye movements and attention, that receives multisensory, cognitive, and arousal inputs from multiple cortical and subcortical areas such as the frontal eye field and locus coeruleus, is implicated underlying these modulations. These results highlight a promising potential of integrating pupil size and saccades to investigate neural, cognitive, and affective processing.