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This study presents levels of Campylobacter spp. and Escherichia coli on broiler carcasses across the slaughter line in three fully automated Danish slaughterhouses with the aim to investigate differences in slaughter hygiene between the lines, correlation between concentrations of E.coli and Campylobacter, and finally, the relationship between Campylobacter counts in caeca and on chilled meat. In total, 15 commercial, indoor flocks were examined and from each flock 24 caecal samples and 24 carcass samples were collected from each of the control points after plucking (AP), after evisceration (AE) and after chilling (AC). Results showed distinct differences between slaughterhouses. For slaughterhouse I the contamination level was high AP and decreased AE while for slaughterhouse II the contamination level was low AP and increased AE. For slaughterhouse III the contamination level varied insignificantly across the processes. Results also showed differences in contamination levels of E. coli and Campylobacter between slaughterhouses. Mean counts of the two organisms increased or decreased concurrently from after plucking to after evisceration within slaughterhouses; however, after chilling counts of E. coli were reduced to a larger extent than counts of Campylobacter. This suggests that for processing of Campylobacter positive broilers E. coli may be used as an indicator of faecal contamination during the processing steps up to the point of chilling but not as an indicator of Campylobacter contamination of chilled broiler meat. A correlation was found, though, between the mean number of Campylobacter in caeca and the mean number of Campylobacter on broiler meat after chilling which means that the level in the gut at slaughter significantly impacts the level on the chilled meat. In conclusion, our data confirm that less faecal contamination throughout processing, and/or less Campylobacter in the gut at the point of slaughter will lead to less Campylobacter contamination on the meat and thereby improve food safety. Exchange of information between slaughterhouses on best hygiene practices and compliance with these is an option to reduce numbers of Campylobacter in broiler meat.