Human Salmonella infections are often associated with the consumption of infected eggs and egg products. Therefore, knowing the prevalence of Salmonella spp. in flocks of laying hens and the factors that influence the occurrence of Salmonella on farms is of the utmost importance. Since 2012, housing laying hens in conventional cages has been prohibited in the European Union, and hens may only be kept in enriched cages or alternative housing systems. The prohibition of conventional cages has improved the welfare of laying hens, but has raised issues concerning the detrimental consequences for the spread and occurrence of infectious diseases in hen flocks. The aim of this study was to analyse the occurrence of Salmonella spp. in laying hen flocks in eastern Croatia in the period from 2020 to 2023, and to determine whether housing systems have an impact on occurrence. During this period, a total of 1534 samples of laying hen faeces from 191 flocks (106 flocks housed in enriched cages and 85 flocks in housing systems with closed outdoor runs) were tested at the Diagnostics Laboratory of the Croatian Veterinary Institute, Veterinary Department Vinkovci, as part of implementation of the National Salmonellosis Control Programme and official sampling in the Republic of Croatia for the presence of Salmonella spp. Isolation, identification and serotyping of Salmonella was conducted in accordance with the standard HRN EN ISO 6579-1:2017/A1:2020 method. Salmonella spp. was confirmed in the faeces of seven laying hen flocks (6.60%) housed in enriched cages, and 11 flocks (12.94%) of laying hens in housing systems with outdoor runs. The research results showed that there was no significant difference in the total occurrence of Salmonella between flocks of laying hens housed in housing systems with outdoor runs and those in enriched cages. The highest percentage of positive flocks was found in 2020 in 11.11% of flocks of laying hens housed in enriched cages and 18.18% of flocks of laying hens kept in housing systems with outdoor runs. When observed by county over the four-year study period, the percentage of positive flocks was significantly higher (P<0.05) in Brod-Posavina County in comparison with Osijek-Baranja County and Vukovar-Srijem County. The research results suggest that there is small possibility that transitioning from enriched cage systems to alternative housing systems, with strict biosecurity measure implementation, would increase Salmonella infections in laying hen flocks.