Recent theories describe perception as an inferential process based on internal predictive models adjusted by means of prediction violations (prediction error). To study and demonstrate predictive processing in the brain the use of unexpected stimulus omissions has been suggested as a promising approach as the evoked brain responses are uncontaminated by responses to stimuli. Here, we aimed to investigate the pupil's response to unexpected stimulus omissions in order to better understand surprise and orienting of attention resulting from prediction violation. So far only few studies have used omission in pupillometry research and results have been inconsistent. This study adapted an EEG paradigm that has been shown to elicit omission responses in auditory and somatosensory modalities. Healthy adults pressed a button at their own pace, which resulted in the presentation of sounds or tactile stimuli in either 88%, 50% or 0% (motor-control) of cases. Results revealed that omission responses were observed in both modalities in the 88%-condition compared to motor-control. Similar pupil omission responses were observed between modalities, suggesting modality-unspecific activation of the underlying brain circuits. In combination with previous omission studies using EEG, the findings demonstrate predictive models in brain processing and point to the involvement of subcortical structures in the omission response. Our pupillometry approach is especially suitable to study sensory prediction in vulnerable populations within the psychiatric field.