Campylobacter is responsible for human bacterial enteritis and poultry meat is recognised as a primary source of infection. In slaughterhouses, cleaning and disinfection procedures are performed daily, and it has been suggested that disinfectant molecules might select for antibiotic resistant strains if shared targets or combined resistance mechanisms were involved. The aim of the study was to investigate if cleaning and disinfection procedures in poultry slaughterhouses select for antibiotic resistance in Campylobacter jejuni and C. coli and to determine the genotypes of isolates collected after cleaning and disinfection. Nine sampling visits were made to four French slaughterhouses. Samples were collected from transport crates and equipment surfaces, before and after cleaning and disinfection. Minimal inhibitory concentrations of the recovered C. jejuni and C. coli isolates to six antibiotics and two disinfectants were measured. The C. jejuni isolates collected from equipment surfaces after cleaning and disinfection were subjected to PCR-RFLP typing. Twenty-five C. jejuni isolates and 1 C. coli were recovered from equipment surfaces after cleaning and disinfection during five visits to three different slaughterhouses. Those isolates did not show an increased resistance to the tested antibiotics compared to isolates collected before cleaning and disinfection. Only one or two genotypes were recovered after cleaning and disinfection during single visits to each slaughterhouse. This observation suggests that such genotypes may be particularly adapted to survive cleaning and disinfection stress. Understanding the survival mechanisms of Campylobacter should facilitate the implementation of better-targeted strategies and reduce the public health burden associated with Campylobacter infection.