The use of conventional battery cages for hens will be prohibited in Germany in 2007. Only few studies, however, have considered the differences between battery cages and alternative systems with regard to infectious diseases. The existing gaps in the current knowledge need to be closed by research and measures must be developed that will prevent the spread of viral, bacterial, and parasitic infections in alternative poultry housing systems. With regard to virus infections, avian influenza requires particular attention. Since wild birds, particularly anseriformes, represent a reservoir for avian influenza viruses, free-ranging poultry is much more at risk of infection than birds in closed hen-houses. Appropriate measures must prevent direct contact with wild birds and transmission via contaminated water, feed, or equipment. Several bacterial infections of poultry represent zoonoses. Salmonella and Campylobacter are considered as particularly important. To avoid a potential increase in the risk of infection for consumers due to poultry keeping systems that might favour infections with bacterial zoonotic agents, there is a special need for research in this area. With regard to parasitic infections, coccidioses may cause problems in alternative poultry housing systems, and lead to considerable economic consequences. The epidemiological situation concerning infections with Histomonas meleagridis needs to be analysed. Since all compounds that had been used for prophylactic or therapeutic purposes in the past have been banned, there is a need to develop new drugs which are safe for animals and humans.