Worldwide, the use of antimicrobials in food production has been associated with drug resistance in foodborne pathogens such as Salmonella. However, little is known about the efficaciousness of fluorequinolone treatment on Salmonella Typhimurium T104 infections in pig breeding herds. A combined eradication procedure with enrofloxacin application on sows and piglets, feeding of encapsulated organic acids to sows, disinfection with peracetic acid, separation of the growers from the sows and serological discrimination using a new whole-cell-based enzyme-linked immnosorbent assay (ELISA) was evaluated for the suitability to eradicate and to control endemic S. Typhimurium DT104 infections in a closed herd. Thirty-seven sows and their piglets were treated everyday from day 14 ante partum until the day of weaning. Eighteen sows and their piglets served as controls. From the first day of life until day 168 after birth, faecal samples (n = 1671) of all piglets were analysed for Salmonella shedding. In parallel, systemic antibody responses were monitored by whole-cell-based isotype-specific ELISA systems. From birth to weaning the prevalence in both groups was between 2% and 9%. After weaning, intermittent shedding could be observed in both groups, and salmonellae could be found in up to 7.7% of the faecal samples. As a result, a dramatic increase in Salmonella-infected growers was observed, as of day 115 after birth, 47.4% of the animals of the treated group were tested positive for S. Typhimurium. Our results indicate that despite long-term antibiosis treatment and optimized hygiene measures, shedding of S. Typhimurium by the sows and the subsequent infection of their offspring could not be effectively prevented. Although it could be not shown that elimination of S. Typhimurium DT104 infection was achieved, the disinfection procedures described and the diagnostic test used are effective instruments to decrease the Salmonella load and to identify individual infected animals. Both of these are important factors for an improved consumer protection.