We constructed annual nitrogen budgets for four years for three watersheds underlain with discontinuous permafrost in interior Alaska. During all years, nitrogen export in stream flow exceeded input from deposition, with loss rate greatest from the two watersheds with the lowest spatial extents of permafrost. Elevated nitrogen export appears to be common in regions with discontinuous permafrost, based on nitrogen concentration in streams spanning a latitudinal gradient in permafrost coverage. This pattern of nitrogen loss is counter to temperate regions, where watersheds retain nitrogen even with elevated atmospheric deposition, and unexpected, given that terrestrial primary production appears to be nitrogen limited.