THE Origin of small regions of extremely acidic (pH<4.5) soils in the Klamath mountains of northern California has long been a mystery. These acidic regions are devoid of coniferous vegetation, although surrounded by healthy coniferous forest. Here we show that the extreme soil acidification is caused by nitrogen inputs from ammonium-containing bedrock. Analyses of soil solution composition and bedrock mineralogy reveal that oxidation of ammonium released from the mica schist bedrock generates high levels of nitric acid. The consequent acidity mobilizes potentially toxic levels of aluminium and causes intense leaching of nutrient cations. In the adjacent healthy forest, plant uptake of nitrate attenuates these effects. We suggest that a natural perturbation (for example a small forest fire) caused initial loss of vegetation from the barren regions. We also suggest that subsequent erosion led to serious nutrient depletion of these soils, and that extreme acidification, potentially toxic levels of aqueous aluminium and nutrient deficiencies resulting from cation leaching played a significant role in preventing regrowth. These results show that geological nitrogen, commonly overlooked in biogeochemical cycling but known to be present in appreciable quantities in certain rocks(1-8), may represent a large and reactive pool which can have significant ecological effects.