The startle response can be used to assess differences in a variety of ongoing processes across species, sensory modalities, ages, clinical conditions, and task conditions. Startle serves defensive functions, but it may also interrupt ongoing processes, allowing for a reorientation of resources to potential danger. A wealth of research suggests that prepulse inhibition of startle (PPI) is an indicator of the protection of the processing of the prepulse from interruption by the startle response. However, protection against interruption by suppressing the startle response may extend to many other ongoing processes, including the higher processing of the startle stimulus itself. Proof of protection would require measuring ongoing processing, which has very rarely been reported. The idea that PPI represents the protection of the earliest stages of prepulse processing can be challenged, since those earliest stages are completed by the time the startle response occurs, so they are not threatened by interruption and need not be protected. The conception of low PPI as indicative of a "gating deficit" in schizophrenia should be made with caution, since low PPI is seen in some, but not all studies of schizophrenia, but also in a range of other disorders and conditions. Finally, startle is often used to probe ongoing processes, but the response also modifies those processes, interrupting some processes but perhaps facilitating others. A deeper understanding of the function of startle and PPI might improve the precision of application of these measures in the investigation of a range of research topics.