Parasites of animals constitute an important part of any ecosystem, including livestock production systems. This chapter summarizes the most important internal parasite infections and problems typically recognized in organic dairy farming, including cryptosporidiosis and coccidiosis in young calves and pasture-borne infections, like gastrointestinal nematodes, lungworms, and liver flukes. Aspects of environmental impact of anti-parasitic drug use are also discussed. Most infections are endemic and inherent to grazing systems and rearing of young stock. However, management decisions will affect the balance between parasites and hosts and in some cases result in disease. Prevention of parasites in organic dairy systems should focus on hygienic measures, grazing management and dietary interventions, and aim for an ecological balance between parasite burden and animal welfare/unavoidable production losses. Whenever management fails, appropriate intervention with or without drugs must take place. Lastly, the authors discuss new directions of research, including bioactive forages, breeding for resistance, and vaccines.