Systems theory differs from classic analytical science by producing statements in the context of a descriptive system rather than seeking to reduce a complex problematic situation to researchable entities. This paper analyzes the validity and applicability of systems theory as a scientific approach towards organic farming. The world-views on which organic farming and systems theory build, respectively, are discussed and the methodological consequences of these world views are clarified. The world-view inherent in organic farming, the ontological level, as reflected in stewardship towards nature, the ethic of animal husbandry, and the cycling processes in nature, is harmonious with the underlying ideas of systems theory as regards a hierarchical structure and a mainly anthropocentric stand. This world-view is not paradigmatically different from the world-view inherent in conventional agriculture but non-consistent with the world-view of deep ecology. The world-view of organic farming acknowledges the wholeness in every system with emerging phenomena we might not perceive on an epistemological level. This world-view also acknowledges that such emerging phenomena occur at the higher levels of the hierarchical structure, which is in accordance with systems theory. Originally, a system was defined by its relations to its environment. However, in order to avoid the potential reductionism that may arise when everything is reduced to the ultimate whole system, it is found necessary also to identify and describe the major mechanisms within each system. It is concluded that meeting this requirement, systems theory can be viewed as an extension of traditional methods as the problems become more complex at higher hierarchical levels. Unfortunately, biologically speaking, we still have a limited knowledge of these mechanisms or processes in organic farming, but one of the challenges of today's science in organic farming is to identify and define these mechanisms on every hierarchical level.