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In the 1996 U.S. Food Safety and Inspection Service's (FSIS) 'Pathogen Reduction; Hazard Analysis and Critical Control Point (PR/HACCP) Systems, Final Rule,' Salmonella was selected for microbiological testing and monitoring. Using data from an FSIS-sponsored survey of meat and poultry slaughter establishments, inspection results, and other establishment characteristics, potential variables affecting pathogen control, as measured by Salmonella test results, were investigated. The analysis data sets included 153 federally inspected young chicken slaughter establishments, of which 111 exceeded half the Salmonella performance standard at least once from 2003 through 2005, and 121 federally inspected pork slaughter establishments, of which 28 exceeded half the Salmonella performance standard. Logistic regression results for young chicken slaughter establishments indicate they were more likely to exceed half the standard if they had higher inspection noncompliance rates (P = 0.10) and older production space (P = 0.10), and were less likely to exceed it if they used a higher percentage of raw poultry inputs purchased from outside sources (P = 0.10). Results for pork slaughter establishments indicate they were more likely to exceed half the standard if they had a higher rate of voluntary microbiological testing (P = 0.08), and were less likely to exceed it if they were larger (P = 0.08) and used a higher percentage of raw pork inputs purchased from outside sources (P = 0.02). In general, indicators of plant characteristics, food safety practices, and management philosophy are associated with different levels of pathogen control performance that vary by species slaughtered