The invention provides methods for certification of carcasses, and for detecting a contaminated carcass and preventing its movement into or across a production area. The inventive methods comprise obtaining, early in the production process (pre-fabrication), a test sample from at least one test location of at least one split-portion of each carcass, wherein the test samples are obtained prior to or during chilling of the respective split portions, before entry thereof in the production chain. Composite test samples are assayed for pathogens or microbes, whereby certification is afforded, or whereby entry of the chilled split-carcass-Lot into the production area is precluded if the corresponding composite-Lot test sample is contaminated. Methods for remedial reconditioning of contaminated split-carcasses are provided, wherein essentially 100% of the carcasses are targeted to the production line. The inventive methods provide substantial public health benefit, and are efficient and economical to implement.