A comparative study of salmonella contamination in eleven commercial hatcheries in the UK was carried out during 1992/93. The sampling protocol involved individual swabbing and culture from surfaces and items of equipment within each premises. This allowed the identification of many areas where salmonella control measures were not successful resulting in a cross-contamination hazard for eggs and chicks. Egg sanitisation and handling methods, design of incubator and whole building ventilation systems, control of dust, fluff and aerosol production, disinfection of surfaces and equipment and handling of waste were areas where improvements could be made. There were examples of successful reduction of salmonella in all key areas and these could be extended to provide general practical protocols for salmonella control. The sampling and culture techniques used in this study required less labour and were more rapid and sensitive than traditional methods so could be used in comparative investigations of other complex high throughput livestock and food processing operations.