Introduction: Salmonella is a major cause of foodborne illness throughout the world. The use of quantitative techniques is important for assessing the risk and determining the capacity of each step of the slaughtering process to decrease or increase bacterial contamination. We aimed to detect and to quantify the presence of Salmonella in Brazilian processing plants by real-time quantitative polymerase chain reaction (qPCR). Methodology: A total of 139 poultry slaughterhouses samples were collected in order to detect to and quantify Salmonella by qPCR. Results: Almost all collection points (3/18), except water from pre-chiller tank, carcasses after pre-chiller, and carcasses frozen at -12ºC for 60 days, and 49% (68/139) of samples were positive for Salmonella. Quantification means varied equally among all of the tested sources, and we could not establish any pattern of variation. A large proportion (52.6%) of cloacal swabs was Salmonella-positive. Also, contamination in transport cages was increased after the cleaning process, indicating that the process was ineffective. The overall prevalence in samples obtained during the slaughtering process was 48.9%, and on the whole rinsed carcasses, this proportion was 50%. The detection of Salmonella in frozen carcasses, even after long periods of storage, indicates that the carcasses are a potential source of infection for consumers. Conclusions: We found that contamination levels remain similar throughout the slaughtering. qPCR proved to be an efficient method for the detection of Salmonella.