Organic farming attempts to ensure animal welfare on the basis of preventive measures. The aim of the present study was to investigate the effects of the production system on animal welfare of dairy cows in organic and conventional farms. The results of the application of the Welfare Quality® protocol for dairy cows shows significant differences between organic and conventional farms while concurrently disclosing considerable differences between farms of the same production system. To further improve the animal welfare situation in organic farming and especially to better include animal health issues, result based components should be included into the current (purely action-oriented) EU organic farming regulation.