Our eyes are never still, even during fixation, exhibiting a rich repertoire of oculomotor behavior, such as microsaccades (small saccades at fixation), spontaneous eye-blinks, ocular drift and pupil dilation. These movements are largely involuntary and appear stochastic and arbitrary but have been found related to cognitive processes and attention. Here I report some of our studies that utilize remote video-based eye tracking for diagnostic purposes. In one study, we analyzed the Oculomotor Inhibition effect (OMI) that typically follow a transient stimulus, and its properties (onset and offset times) reveal the time course of the visual processing involved. We used this effect to assess visual contrast sensitivity by just analyzing the onset times of microsaccades in individuals while passively viewing 1Hz contrast flashes. In a second study, we used a similar method to assess ADHD, where we found reduced oculomotor inhibition that normalized with medication. In a third study, we used both the OMI effect and the analysis of visual tracking quality to assess the clinical condition of people with Disorder of Consciousness following brain injury. Finally, we analyze small possibly unintentional saccades to assess the cognitive skills of non-verbal and severely autistic individuals. Overall, our studies demonstrate that the analysis of eye movements and especially the involuntary ones, is a promising tool for assessing motor, perceptual and cognitive functioning in passive viewing, especially considering the growing availability of video-based eye tracking.