Rat strain differences in the acoustic startle response (ASR) and prepulse inhibition (PPI) of that response are of increasing interest, especially as the genetics of PPI may provide an approach to studying the genetics of certain mental illnesses. However, strain differences in PPI are confounded by differences in ASR. To clarify this issue, the authors investigated the ASR and PPI across a range of startling stimulus intensities (70 dB-120 dB) in Wistar and Sprague-Dawley rats (N = 96). Sprague-Dawleys showed more PPI of ASR capacity (response limit) than Wistars. In contrast, Wistars exhibited greater PPI than Sprague-Dawleys, as measured by an increase in response threshold. This dissociation suggests that PPI is more complex than that assessed by single startling stimulus intensity.