Between 1992 and 2003, a period of 12 years after the definitive ban on battery cages in Switzerland, more than 10,000 replacement chicks and laying hens were examined postmortem. There was a significant decrease in the incidence of viral diseases, mostly due to a reduction in Marek's disease, but there was a marked increase in bacterial diseases, particularly since 1999, mainly due to colisepticaemia in young laying hens. There was a steady decrease in parasitic infections, but the incidence of non-infectious diseases varied from year to year, with no clear trends. There were no significant emerging diseases or economic losses in the alternative housing systems. Vaccination and hygiene were the most effective precautions against infections, and control strategies brought about a marked decline in notifiable diseases, especially for Salmonella Enteritidis. Fifteen years after the ban on battery cages in Switzerland, the health and egg production of laying hens is good.