In the present study 66 layer flocks housed in different alternative husbandry systems were monitored from placement of birds on the farm until slaughter to evaluate a possible influence on the occurrence of selected non-infectious as well as infectious diseases. Postmortems were performed and the occurrence of extraintestinal Escherichia coli and Gallibacterium anatis was investigated. No specific postmortem findings were seen in pullets. Non-infectious diseases were mainly found in layers.