Disruption of the early stages of information processing in limbic brain circuits may underlie symptoms of severe neuropsychiatric disorders. Prepulse inhibition of acoustic startle (PPI) is diminished in many of these disorders and may reflect the disruption of this CNS function. PPI is associated with brain activity in many of the same regions in humans as it is in laboratory animals, suggesting that neuroimaging studies in humans may help localize deficits that can then be elucidated in animal models. In this article, we employed a rapid presentation event-related design during continuous EPI BOLD scanning to examine hemodynamic response functions (HRFs) associated with PPI. Fourteen healthy participants listened to 100 pulse alone and 100 prepulse combined with pulse (prepulse-pulse) trials. PPI is the normalized difference in the startle response to the two trial types. Following the prepulse-pulse trials, the amplitudes of the HRFs in auditory cortices and in the anterior insula were increased, while in the cerebellum, thalamus and anterior cingulate, they were decreased, relative to the pulse alone trials. In addition, the timing of the prepulse-pulse responses was delayed in the auditory cortices, anterior insula and cerebellum. Finally, PPI measured outside the scanner was predicted by the difference in BOLD responses between trial types in the anterior insula and in the cerebellum. The results suggest that prepulse inhibition, and by extension early stages of information processing, modulate both the amplitude as well as timing of neural activity.