This field study aimed to establish a risk-orientated hygiene analysis on two broiler farms in Northwestern Germany for the practical use in broiler housing to evaluate the success of disinfection procedures for eradicating S. Java. The risk-orientated hygiene analysis enables fast, reproducible and cost-effective testing of broiler farms and in turn helps minimize the public health risk ensuing from S. Java. Farms were tested before and after cleaning as well as after disinfection according to a risk-orientated hygiene analysis for the presence of Salmonella DNA with qPCR. Positive PCR samples were confirmed by classical microbiology. Before cleaning, all checkpoints were tested positive for Salmonella DNA. Salmonella reduction of ca 66% of the sampled points could be achieved by intensive cleaning. A first disinfection on farm A and B failed to completely eradicate S. Java. A second disinfection followed and finally achieved a Salmonella-free status of the barns. During nine rearing periods, farms were tested weekly with boot swabs for Salmonella and at slaughter carcasses were tested for Salmonella status. No Salmonella were detected in these examinations. The two studied broiler farms have, to date, remained free of Salmonella.