The involvement of cytokinins (CTKs) in the repression of phosphate (Pi)-starvation signalling has been widely documented. However, the full physiological and molecular relevance of this role remains unclear. To gain further insights into the regulation system of CTK repression of Pi-starvation signalling, a global analysis of gene expression events in rice seedlings under Pi starvation, and the exogenous CTK treatment under Pi-sufficient (+P) and Pi-deficient (-P) conditions, was conducted using oligonucleotide array analysis. Physiological and biochemical adaptation was observed after 10 d Pi starvation in rice seedlings. A global reduction of the Pi-starvation signalling was detected after 3 d treatment of exogenous CTK. Expression profiling data indicate that, together with a significant increase of intracellular Pi content, many expression changes responsive to Pi starvation were reversed by exogenous CTK treatment while CTK-responsive genes behaved normally under -P condition. These results suggest that the interplay of CTK signal and Pi-starvation response can be partially explained by the rise of Pi concentration after exogenous CTK treatment. Microarray data also revealed that a small number of genes have different CTK response patterns under different Pi levels, suggesting a subtle interaction between CTK and Pi-starvation signalling pathway.