Inhibitory measures such as prepulse inhibition of the acoustic startle reflex (PPI) and event related potential P50 suppression have been widely reported to show deficits in schizophrenia patients. The relationship between PPI and P50 suppression in schizophrenia patients has remained unclear. One hundred fifty-six schizophrenia patients and 104 normal comparison subjects (NCS) were tested on PPI and P50 suppression. Eighty-one patients and 70 NCS had valid and scorable data on both PPI and P50 suppression paradigms. As in the larger groups, these cohorts had deficits on both PPI (p < .05) and P50 suppression (p < .05). Analyses revealed a weak, but significant correlation between PPI and P50 suppression in the NCS group (r = .33, p < .05) but not in the patient group (r = .03, ns). Although PPI and P50 suppression were both reduced in the patients, they were not correlated. This divergence suggests that these gating functions are complementary or redundant levels of "protection" against processes that may lead to cognitive fragmentation.