In this study, we evaluated the Salmonella detection capability and compatibility of a LightCycler polymerase chain reaction (LC PCR) system with two bacteriological methods, United States Food and Drug Administration's Bacteriological Analytical Manual Chapter 5: Salmonella (FDA) and International Organization for Standardization Method 6579 (ISO). The aim was to determine which bacteriological method would support LC PCR for testing naturally contaminated poultry and red meat samples with Salmonella. Twenty three (50.0%) and 24 (52.2%) out of 46 chicken meat samples were positive for Salmonella by the FDA and ISO methods, respectively. Five of the 15 (33.3%) turkey meat samples were found to harbor Salmonella by both bacteriological methods. None of the red meat samples were positive for Salmonella using the FDA method. There was one red meat sample (3.3%) positive for Salmonella using ISO method. LC PCR results indicated that 23 (50.0%) and 31 (67.4%) of the DNA templates obtained from the 46 preenriched chicken meat FDA and ISO samples were positive for Salmonella. Salmonella detection rate from turkey meat samples by ISO LC PCR was 6.7%, whereas no detection was observed by FDA LC PCR. FDA LC PCR detection rate in red meat samples was 23.3%, whereas the ISO LC PCR was 43.3%. Relative accuracy rates of ISO LC PCR and FDA LC PCR were 67.4%, 60.0%, 53.3% and 56.5%, 66.7%, 76.7% for chicken, turkey, and red meats, respectively. We presume that the low relative accuracy problem, which can be related to the use of FDA and ISO preenrichments for template preparations in the PCRs, can be overcome by the use of primary enrichments of both FDA and ISO bacteriologies.