Nitrogen (N) and phosphorus (P) are essential elements for life, but in excess they contribute to aquatic eutrophication. The Baltic Sea is a brackish semi-enclosed sea that is heavily influenced by anthropogenic loading of nutrients, resulting in a major environmental problem, eutrophication. In this study, the nutrient balance of the food production and consumption system in seven countries in the Baltic Sea drainage area was quantified for the period 2002-2005. The food production and consumption system accumulates nutrients in the Baltic Sea drainage area, due to extensive imports to the system. The average annual net surplus of nutrients was 1,800,000 tons N and 320,000 tons P in 2002-2005, or annually 28 kg N and 5 kg P per capita. The average total annual import was 2,100,000 tons N and 340,000 tons P during 2002-2005. The largest imports to the system were fertilizers, totaling 1,700,000 tons N and 290,000 tons P. Traded nutrients in food and fodder amounted to a net annual surplus of 180,000 tons N and 25,000 tons P. The nutrient load to the Baltic Sea due to the food consumption and production system was 21% N and 6% P of the respective annual net inputs to the region. This study shows that large amounts of nutrients to Baltic Sea drainage area are inputs from outside the region, eventually contributing to eutrophication. To reduce the nutrient imports, fertilizers should be used more efficiently, nutrients should be recycled more efficiently inside the region, and food system should be guided toward low-nutrient intensive diets.