A thorough understanding of nitrate (NO3-) leaching is needed to optimize fertilizer management for reducing groundwater contamination by NO3- while maintaining crop yields. The objective of this study was to determine the effects of the long-term application of different N sources on NO3- distribution in deep soil profiles up to 4.5 m in Japanese Andisols with a high anion exchange capacity (AEC). Crops of sweet corn (Zea mays L.) and Chinese cabbage (Brassica rapa L. var. amplexicaulis) were grown each year during the period from 1994 to 2004 in fields subjected to four different types of treatment with N: pig compost (PC), ammonium N (AN), coated urea (CU), or no fertilizer (NF). Nitrate concentrations in soil water at 1-m depth increased markedly in Year 2 and fluctuated between 30 and 60 mg N L-1 in AN and CU plots through the experimental period. In the PC plot, NO3- concentration started increasing in Year 4 and reached to the same level in Year 6 as in AN and CU plots. Soil NO3- contents were often more than 100 mg N kg-1 between 1- and 2.5-m depths in the N added plots, and were the highest in the AN treatment, where NO3- leaching was the greatest during the experiment. In the N added plots, the highest soil NO3- contents were seen at 2.5-m depth due to lower soil sulfate (SO42-) content and lower pH than those within the 0.5-2 m layers. Less soil SO42- increased NO3- adsorption in soil at 2.5 m, because SO42- adsorption is more competitive than NO3-. Lower soil pH should exert a higher AEC at 2.5 m. Our results suggest that in Japanese Andisols, NO3- is leached out of root zones within several years, but much NO3- will be retained by absorption in deep layers, regardless of whether the added N is organic or inorganic.