The acoustic startle reflex (ASR), a defensive response, is a contraction of the skeletal and facial muscles in response to an abrupt, intense (> 80 db) auditory stimulus, which has been extensively studied in rats and humans. Prepulse inhibition (PPI) of ASR is the normal suppression of the startle reflex when an intense stimulus is preceded by a weak non-starting pre-stimulus. PPI, a measure of sensory motor gating, is impaired in various neuropsychiatric disorders, including schizophrenia, and is modulated by cognitive and emotional contexts such as fear and attention. We have modeled the fear modulation of PPI of ASR based on its anatomical substrates and taking into account data from behaving rats and humans. The model replicates the principal features of both phenomena and predicts underlying neural mechanisms. In addition, the model yields testable predictions.