Since the 1980s, the prevalence of Salmonella in Belgian poultry layers and broilers has greatly fluctuated with a rise observed in 2003 and a significant decrease in 2005. In order to alleviate the risk at egg consumer level, it is crucial to understand the factors which influence the contamination and the spread of Salmonella in laying hens. To study such determinants we explored the Belgian data from the 2005 baseline study on the prevalence of Salmonella in laying flocks of Gallus gallus in the European Union. The response variables corresponded to presence or absence of Salmonella from dust and faecal samples taken from the environment of a Belgian layer flock. The explanatory variables included: region of Belgium, sampling time (month the flock was sampled), production type (cage or barn and free range), Salmonella vaccination status, flock age and flock size. Analyses of these data were performed using a bivariate logistic regression model assuming independence between the two responses and bivariate generalized estimating equations model, which incorporates the correlation between the two responses on the same flock. The main risk factor that was identified was rearing flocks in cages compared to barns and free-range systems. The results also showed a significant higher risk for Salmonella for a 1 week increase in flocks' age as well as with a unit increase in the size of the flock.