The objectives of this study were to identify factors associated with Salmonella status at the farm, pen, and pig level; explore the nature of variation in the association between the pen-level Salmonella status and pen-level covariates, and pig-level Salmonella status and pig- and pen-level covariates; and to identify the relative importance of factors operating at geographical, farm, and pen level for Salmonella shedding of pigs. For these purposes, samples from 799 pigs and 374 pens on 80 farms in Ontario in 2004 were collected and bacteriologically tested in a cross-sectional study. Census division was the least variable level, and farm the most variable level for shedding. Increased frequency of disinfection and washing with cold water were positively associated with Salmonella positivity, whereas liquid and mash feed and completely closed barns were sparing factors. After farm, pen was the second most variable level for shedding. However, no measured pen-level variables were associated with Salmonella status of pigs or pens. The shedding of Salmonella at the pig level tended to be associated with pig weight, and there was no random variation around this association. Results of this study suggest that a herd test based on bacteriological culture would probably have higher sensitivity if growing animals of lower weight were sampled instead of market weight animals, and this might be beneficial for Salmonella monitoring.