Parasites of animals, and plants as well, constitute an important part of any ecosystem. In fact, 50% of all living species have a lifestyle that can be regarded as parasitic (Poulin and Morand, 2004), and parasites comprise up to 3% of the total biomass in certain estuarine ecosystems (Kuris et al., 2008). Parasites are also an inevitable part of any livestock production system. Although organic farming as a principle aims for natural living (Hovi et al., 2003; Lund, 2005), there will be inherent restrictions imposed due to, e.g. limited space, age structure of animal flock or herd and nutrition, which make it different from natural ecosystems. These factors will affect the balance between parasites and hosts, and in some cases result in disease. Some parasite infections affect only a few farms, and can be limited by biosecurity measures, whereas other infections are endemic and inherent to grazing systems and are therefore difficult, or impossible, to avoid. The management in organic dairy systems should aim for an ecological balance between parasite burden and animal welfare/ unavoidable production losses, and when needed, appropriate intervention (Thamsborg and Roepstorff, 2003). This chapter will briefly summarize the most important parasite infections and problems recognized in organic dairy farming – many of these are well known from conventional farming but levels and interventions may be different. Furthermore, we will discuss new directions in research within this area of organic dairy farming.