The ability of plants to sense available nutrients in the soil and to respond accordingly is of fundamental importance for their adaptation to the environment. The plasticity of root in development in response to nitrogen (N) deficiency is vital, as N is a major nutrient essential for plant growth and development. Changes in root morphology under the stress of N deficiency are complex and vary with experimental conditions and plant species. Little attention has been paid to root growth under the stress of N deficiency, possibly because of the inconsistent response of primary root in length to N deprivation depending on plant age and N concentration supplied. Thus root morphology in rice under the stress of N deficiency has not yet been characterized in detail. Root formation is regulated by both environmental conditions and intrinsic factors. Auxins play a key role in rice plants establishing and developing root morphology. Few studies have evaluated the role of auxins in regulating root growth under low N conditions. To what extent, if any, auxin transport in rice roots is regulated by N deficiency remains unclear. In this paper, a hydroponic media experiment was carried out on N concentration regulating auxin transport and relationship between root formation and transport and distribution of auxins in rice. In this study, biomass, N concentration, seminal root length and lateral root density (LR density) of rice plants and auxin concentration in the plant and relative expression of OsPIN family genes of auxin outflowing protein were investigated relative to N concentration (0.01, 0.2, 1, 2.5 and 5 mmol L^-1) in hydroponic media. Comparison of the plants under two N concentrations (0.01 and 2.5 mmol L^-1) reveals that the ratio of root to shoot increased significantly with decreasing N concentration, partly resulting from decline of the plant root in biomass relative to shoot. However, compared with the plants under normal N concentration (2.5 mmol L^-1), the plants under low N concentration (0.01 mmol L^-1) were 33% lower in root N concentration, 25% longer in length of seminal root and 26% lower in lateral roots density. Besides, the latter were 140% higher in auxin concentration in the 1st leaf from the top but 22% and 60% lower, respectively, in the root-shoot junction and the root, indicating that N deficiency probably resulted in inhibition of auxin polar transport from the shoot to root. RT-PCR analysis shows that the relative expression of OsPIN1a-b、OsPIN2、OsPIN5a-b and OsPIN9 markedly decreased in rice root of the plants under the stress of low N concentration as compared with their respective one in the plants under normal N concentration. Application of exogenous 1-Naphthaleneacetic acid ( NAA)，to plants under the stress of low N concentration inhibited growth of their seminal root in length, but stimulated growth of their lateral roots on seminal root in density to form a root system structure similar to that of the plants under normal N concentration, while application of N-1-naphthylphthalamic acid (NPA), a kind of auxin transport inhibitor to plants under normal N concentration stimulated growth of their seminal in length, but inhibited growth of their lateral root density on seminal root to form a root system structure similar to that of the plants under the stress of low N concentration. It could, therefore, be concluded that the inhibition of polar transport of auxin from the first leaf next to the top down to root in the plant by N deficiency was one of the physiological mechanisms of the response of rice roots to the stress of N deficiency.