In 2005, The International Federation of Organic Agricultural Movements (IFOAM) developed four new ethical principles of organic agriculture to guide its future development: the principles of health, ecology, care, and fairness. The key distinctive concept of animal welfare in organic agriculture combines naturalness and human care, and can be linked meaningfully with these principles. In practice, a number of challenges are connected with making organic livestock systems work. These challenges are particularly dominant in immature agro-ecological systems, for example those that are characterized by industrialization and monoculture. Some of the current challenges are partly created by shortages of land and manure, which encourage zero-grazing and other confined systems. Other challenges are created in part by the conditions for farming and the way in which global food distribution systems are organized, e.g., how live animals are transported, how feed is traded and transported all over the globe, and the development of infrastructure and large herds. We find that the overall organic principles should be included when formulating guidelines for practical organic animal farming. This article explores how the special organic conceptions of animal welfare are related to the overall principles of organic agriculture. The aim is to identify potential routes for future development of organic livestock systems in different contexts and with reference to the specific understanding of animal welfare in organic agriculture. We include two contrasting cases represented by organic livestock systems in northwestern Europe and farming systems in tropical low-income countries; we use these cases to explore the widely different challenges of organic livestock systems in different parts of the world.