Increasing nitrogen (N) and phosphorus (P) inputs have greatly contributed to the increasing food production in China during the last decades, but have also increased N and P losses to the environment. The pathways and magnitude of these losses are not well quantified. Here, we report on N and P use efficiencies and losses at a national scale in 2005, using the model NUFER (NUtrient flows in Food chains, Environment and Resources use). Total amount of "new" N imported to the food chain was 48.8 Tg in 2005. Only 4.4.Tg reached households as food. Average N use efficiencies in crop production, animal production, and the whole food chain were 26, 11, and 9%, respectively. Most of the imported N was lost to the environment, that is, 23 Tg N to atmosphere, as ammonia (57%), nitrous oxide (2%), dinitrogen (33%), and nitrogen oxides (8%), and 20 Tg to waters. The total P input into the food chain was 7.8 Tg. The average P use efficiencies in crop production, animal production, and the whole food chain were 36, 5, and 7%, respectively. This is the first comprehensive overview of N and P balances, losses, and use efficiencies of the food chain in China. It shows that the N and P costs of food are high (for N 11 kg kg(-1), for P 13 kg kg(-1)). Key measures for lowering the N and P costs of food production are (i) increasing crop and animal production, (ii) balanced fertilization, and (iii) improved manure management.