Phosphorus is one of the essential macronutrients required for plant growth and development. The plants increase the absorption of phosphorus through an expansion of the root system in the soil when they are in low-phosphorus conditions. At the same time, the changes in biochemical metabolic pathways and the increase of secretion of phosphatase and organic acids activate the insoluble phosphate fixed in the soil. The expression profile in response to low phosphorus was investigated for rice at 6, 24 and 72 h after low-phosphorus stress compared with normal phosphorus conditions as a control with DNA chip. A total of 1207 differen- tially expressed genes were found in our study; 795 and 450 genes exhibited alterations in their RNA expression in response to inorganic phosphate (Pi) starvation in at least one of the three time points in roots and shoots. Thirty-eight genes overlapped in shoots and roots. The functional classification of these genes indicated their involvement in various metabolic pathways, ion transport, signal transduction, transcriptional regulation, and other processes related to growth and development. A large number of transposable elements changed the expression in rice after low-phosphorus stress. The results may provide useful information about molecular processes associated with Pi deficiency and facilitate the identification of key molecular determinants for improving Pi use by crop species. Phosphorus is one of the essential macronutrients required for plant growth and development. The plants increase the absorption of phosphorus through an expansion of the root system in the soil when they are in low-phosphorus conditions. At the same time, the changes in biochemical metabolic pathways and the increase of secretion of phosphatase and organic acids activate the insoluble phosphate fixed in the soil. The expression profile in response to low phosphorus was investigated for rice at 6, 24 and 72 h after low-phosphorus stress compared with normal phosphorus conditions as a control of DNA chips. A total of 1207 differen- tially expressed genes were found in our study; 795 and 450 genes exhibited alterations in their RNA expression in response to inorganic phosphate (Pi) starvation in at least one of the three time points in roots and shoots. Thirty-eight genes overlapped in shoots and roots. The functional classification of these genes showed their involvement in various m etabolic pathways, ion transport, signal transduction, transcriptional regulation, and other processes related to growth and development. A large number of transposable elements changed the expression in rice after low-phosphorus stress. The results may provide useful information about molecular processes associated with Pi deficiency and facilitate the identification of key molecular determinants for improving Pi use by crop species.