Sensorimotor gating of the startle reflex can be studied in humans and laboratory animals using measures of prepulse inhibition (PPI) of the startle reflex. PPI is reduced in patients with specific neuropsychiatric disorders and in rats after manipulation of the limbic cortex, striatum, pallidum or pontine tegmentum. Studies are rapidly identifying the neurochemical and neuroanatomical substrates regulating PPI in laboratory animals; this detailed circuit information has been used as a ‘blueprint’ to identify possible candidate substrates responsible for PPI deficits in psychiatrically disordered humans. In parallel, studies have also begun to assess the homology of pharmacological effects on PPI across species, as an initial step towards translating detailed neural circuit information from rats to humans. Despite this rapid progress, there is an increasing danger of overlooking important methodological and interpretative issues that could impact either positively or negatively on the ultimate utility of models based on measures of PPI. Some of these issues — ranging from the cross-species methods for quantifying specific variables to the relevance of genetic drift to animal and human studies of PPI — and their implications for future studies are the focus of this review.