A 3-year longitudinal study was conducted on a multi-site farrow-to-finish production system. For each of 18 cohorts at three finishing sites, 50 pigs were randomly selected. Faecal samples were collected every 2 weeks for 16 weeks. Salmonella was cultured from 453 (6·6%) of 6836 faecal samples. The pig-level incidence of Salmonella was 20·8% (187/899 pigs). Salmonella prevalence varied between cohorts and within pigs. The adjusted Salmonella prevalence decreased over the finishing period from 6·4% to 0·8%. Intermittent detection of Salmonella was found in more than 50% of pigs that were positive at more than one collection. The finding that the majority of pigs shed intermittently has implications for surveillance and research study design when determining Salmonella status. The variability in shedding over time, as well as between and within cohorts and pigs suggests that there may be time-variant risk factors for Salmonella shedding in swine.