The increase in the ratio of root growth to shoot growth that occurs in response to phosphate (Pi) deprivation is paralleled by a decrease in cytokinin levels under the same conditions. However, the role of cytokinin in the rescue system for Pi starvation remains largely unknown. We have isolated a gene from Arabidopsis thaliana (AtIPS1) that is induced by Pi starvation, and studied the effect of cytokinin on its expression in response to Pi deprivation. AtIPS1 belongs to the TPSI1/Mt4 family, the members of which are specifically induced by Pi starvation, and the RNAs of which contain only short, non-conserved open reading frames. Pi deprivation induces AtIPS1 expression in all cells of wild-type plants, whereas in the pho1 mutant grown on Pi-rich soils, AtIPS1 expression in the root was delimited by the endodermis. This supports the view that pho1 is impaired in xylem loading of Pi, and that long-distance signals controlling the Pi starvation responses act via negative control. Exogenous cytokinins repress the expression of AtIPS1 and other Pi starvation-responsive genes in response to Pi deprivation. However, cytokinins did not repress the increase in root-hair number and length induced by Pi starvation, a response dependent on local Pi concentration rather than on whole-plant Pi status. Our results raise the possibility that cytokinins may be involved in the negative modulation of long-distance, systemically controlled Pi starvation responses, which are dependent on whole-plant Pi status.