The objective of this study was to relate R-phycoerythrin (PE) fluorescence decay to the inactivation of Salmonella in beef patties cooked using adequate and inadequate thermal processes as defined by the U.S. Department of Agriculture (USDA) safe harbor requirements and lethality standards. Ground beef containing 4.8 or 19.1% fat was inoculated with an eight-strain cocktail of Salmonella and formed into 113-g patties. Capillary tubes containing PE in borate buffer at pH 9.0 were attached to a thermocouple and inserted horizontally into the patties. Patties (n = 43) were cooked on a grill maintained at 177 degrees C for 6 to 13 min and reached internal temperatures ranging from 57 to 77 degrees C. Patties were analyzed for Salmonella survivors and for fluorescence decay of PE. The thermal lethality of each process was calculated at a reference temperature of 65 degrees C. Twenty-four of the 43 high-fat patties met the USDA safe harbor regulations, with thermal lethalities of >66 s, whereas only 20 of these patties met the proposed 5-log10 lethality standard. Three of the 20 low-fat patties that met USDA regulations did not meet the proposed lethality standard. A normalized PE fluorescence value of about 0.3 (confidence interval = 99%) indicated that patties had been processed sufficiently to reduce Salmonella by 5 log10 cycles. PE has the potential for use as a marker to verify processing adequacy in food-processing plants and in other settings in which the use of the target pathogen is inappropriate.