Phosphorus (P) is an important structural component and plays critical roles in the process of energy transfer and signal transduction. Effect of low P on carbohydrate metabolism was investigated at the transcription level via transcriptome analysis using the rice 60K oligonucleotide DNA microarrays. Two-week-old rice seedlings were grown under a low (32 μM) or high (320 μM) P condition for two weeks and leaves from the seedlings were used for transcriptome analysis. Expression of genes involved in carbohydrate metabolic pathways (eg. glycolysis, sucrose degradation and starch synthesis and degradation) was most significantly affected under low P. Under low P, most genes involved in glycolysis were intensively down-regulated, genes of starch biosynthesis and degradation pathway were up- or down-regulated, and many genes involved in sucrose biosynthesis were intensively up-regulated. In leaves under low P, glucose and pyruvate levels decreased, but sucrose and starch levels increased. These results suggest that carbohydrate metabolism is adjusted primarily through comprehensive transcriptional modulation of genes involved in the carbohydrate metabolic super-pathway.