The purpose of this study was to evaluate the transmission of pathogenic respiratory bacteria to thirteen 5-month-old specific pathogen free (SPF) pigs, during the slaughtering process in a commercial slaughterhouse. Before transportation, the SPF pigs and the lorry were checked to confirm the absence of pathogenic respiratory bacteria. Nine SPF pigs (group 1) were in contact in a conventional slaughterhouse with finishing pigs, during 4h before slaughtering. Four SPF pigs (group 2) were slaughtered immediately at arrival in the slaughterhouse. Five bacterial pathogens (Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, Pasteurella multocida, Haemophilus parasuis and Streptococcus suis) were detected by PCR, after slaughtering, from nasal cavities, tonsils and trachea in the two groups of pigs. Lung samples were PCR negative. Three and four bacterial species were isolated from the pigs of group 2 and group 1, respectively. Cultures were negative from the lungs. All the bacterial species present in the SPF pigs were detected by PCR. P. multocida was isolated, from three samples of scalding water before the onset of slaughtering. Our results suggest that the SPF pigs became contaminated mainly by the slaughterhouse environment and the scalding water. Histological examinations revealed that during scalding, contaminated water could reach the trachea and the lungs of pigs. Checks conducted at slaughter for respiratory disorders have to be carried on, but nasal cavities and tonsils are not appropriate for bacteriological investigations. Moreover, bacteriological results obtained from the lungs of slaughtered pigs have to be used with carefulness.