Whereas early organic farming was mainly focused on plant production, in the last decade, the number of organically-managed poultry farms within the European Union has increased significantly. Similar to organic crop production, organic animal farming is based on the same principles: welfare-friendly, sustainable production and resource utilisation without or with very little addition of synthetic substances, such as antibiotics and antiparasitic treatments. These practices, as well as the access to wild animals, make the free-range poultry production systems predisposed to different viral diseases and, thus, associated with potentially higher public health risks or reduction in production quality. On the other hand, intensive farming amplifies the impact of viral diseases due to high density, low genetic diversity and elevated immunodeficiency. The aim of this analytical study is to compare free-range with intensive poultry systems and the occurrence of different viral diseases in these types of farms in the EU over the past decade. The research is based on official data from the statistical office of the European Union, as well as official data from the Member countries. The results were similar in each country and demonstrate that free-range production has a higher incidence of viral diseases with high zoonotical potential. This makes year-round surveillance absolutely necessary, as well as the need for implementation of additional criteria and requirements towards free-range systems.