Salmonella outbreaks in humans are often linked with the consumption of contaminated eggs. Therefore a profound knowledge of the actual prevalence of Salmonella spp. in laying hens and the factors that influence the presence and persistence of Salmonella on a farm is of utmost importance. The housing of laying hens in conventional battery cages will be forbidden in the European Union (EU) from 2012 onwards. There is an urgent need to evaluate whether this move to alternative housing systems will influence the prevalence of Salmonella in laying hens. Therefore, a cross-sectional study was performed in 5 European countries (Belgium, Germany, Greece, Italy and Switzerland) to determine the between and within flock prevalence of hens shedding Salmonella and to investigate whether there is an effect of the housing type on Salmonella prevalence. In total 292 laying hen farms were sampled in the month prior to depopulation. An on-farm questionnaire was used to collect information on general management practices and specific characteristics of the sampled flock. Twenty-nine flocks were found positive for at least 1 Salmonella-serotype. In these flocks the within flock prevalence of shedding hens, determined by individual sampling of 40 hens, varied between 0% and 27.50%. A wide variety of serotypes was isolated with Salmonella Enteritidis as the most common. Housing in conventional battery cages, the absence of dry cleaning in between production rounds and sampling in winter turned out to be risk factors for the shedding of Salmonella Enteritidis or Typhimurium (P <0.05).