1. Selected health and welfare variables of laying hens from 79 flocks kept in alternative husbandry systems were assessed at the end of lay. 2. Investigations were carried out on 100 hens per flock at the slaughter line and recorded as part of a novel scoring system. In addition, post-mortem investigations as well as parasitological examinations were conducted on 10 birds from each flock. 3. Birds with access to free range had better plumage than birds kept in barn systems. Housing in aviaries was associated with a higher prevalence of foot pad lesions and keel bone deformations. In addition, poorer plumage, more and worse skin and foot pad lesions were documented in hens slaughtered during the winter months. 4. Oophoritis and/or salpingitis were the most prevalent pathomorphological changes observed. Intestinal parasites, especially Heterakis gallinarum and Ascaridia galli, were frequent. Hens kept indoors had fewer nematoda and cestoda than those from conventional and organic free range. 5. The slaughterhouse protocol allowed direct comparison of variables between flocks and specific problems to be identified in particular flocks. The results could be used to initiate detailed investigations into problematic issues on selected farms.