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There is much current interest in the potential role of agroforestry in the mitigation of nutrient depletion in Sub-Saharan Africa. Using data from farm surveys and trials, a static model of N and P flows was constructed for a standard farm system, representative of typical subsistence farms in humid parts of the East African Highlands. The model was used to explore the possible impact of improved agroforestry systems on nutrient budgets, to identify priorities for research. Soil nutrient balances in the standard farm system were - 107 kg N and - 8 kg P ha−1 yr−1. Agroforestry systems did not significantly reduce the N deficits except when a high proportion of the total biomass was returned to the soil, rather than removed from the farm. Agroforestry increased N input through biological N fixation and deep N uptake, but this was offset by a larger nutrient removal from the farm in harvested products, which increased from 38 kg N in the standard system to 169 kg N ha−1 yr−1 in an intensive dairy-agroforestry system. Agroforestry did not increase P inputs, and harvested P increased from 6 kg P in the standard farm system to 29 kg P ha−1 yr−1 in the dairy-agroforestry system. Thus, moderate P inputs, of 20 kg P ha−1 yr−1 were required to maintain soil P stocks. N leaching from the field was the most significant nutrient loss from the farm system, with a range of 68 to 139 kg N ha−1 yr−1. The capture of subsoil N by deep-rooted trees in agroforestry systems substantially increased N-use efficiency, providing 60 kg N ha−1 yr−1 in the dairy-agroforestry system. The budgets were sensitive to N mineralization rates in subsoils, N losses from soils and manures, and effectiveness of deep-rooted plants in subsoil N capture, for which there is little data from the region. Therefore, high priority should be given to research in these areas. The current model can not account for important feedback mechanisms that would allow analysis of the long-term effects of nutrient budgets on nutrient availability and plant productivity. Dynamic models of farm nutrient budgets that include such interactions are needed to further assess the sustainability of farming systems. more...