An important food safety issue in the slaughterhouse is flock to flock contamination.

Chickens may carry potentially pathogens and should therefore be monitored prior to slaughter in such way that the results are available before the animals are loaded. Flocks contaminated with Salmonella and/or Campylobacter should be slaughtered separatly from the uncontaminated flocks. The pathogen free flocks should be slaughtered, followed by the contaminated flocks; the so called "logistic processing". At the end of every slaughter day or shift the equipment should be cleaned and disinfected.
Not only the animals but also the transportation equipment (trucks, containers, boxes) and the  crew should be free of pathogens. Whether chickens are delivered wet or dry is a main issue regarding cross contamination at the slaughterhouse plant. When chickens are moist, microbes can easily attach to the chcicken skin. Moist chickens may be more contaminated with manure, which contains high numbers of microbes (e.g. Salmonella, Campylobacter, but also general spoilage micro-flora), and therefore dry chickens are preferred.

In order to gain a hygienic slaughtering process, the feed withdrawal period should be observed. Roughly the time to digest the residual feed for chicken is estimated at 8 hours.

Food safety issues: Cross-contamination between flocks