The metabolism of phosphoinositides plays an important role in the signal transduction pathways. We report here that naturally occurring polyamines affect the activities of phosphatidylinositol (PI) 3-kinase and PI 4-phosphate (PIP) 5-kinase differently. While polyamines inhibited the PI 3-kinase activity, they stimulated the activity of PIP 5-kinase in the order of spermine > spermidine > putrescine. Spermine inhibited the PI 3-kinase activity in a concentration-dependent manner with an IC50 of 100 microM. On the other hand, spermine (5 mM) stimulated the activity of PIP 5-kinase 2-3 fold. Kinetic studies of spermine-mediated inhibition of PI 3-kinase revealed that it was noncompetitive with respect to ATP. The effect of Mg2+ and PIP2 concentration on kinase activity was sigmoidal, with spermine inhibiting PI 3-kinase activity at all PIP2 concentrations. While 1 mM calcium stimulated PI 3-kinase activity at submaximal concentrations of Mg2+ (1.25 mM), inhibition was observed at optimal concentration of Mg2+ (2 mM). We propose that spermine may modulate the cellular signal by virtue of its differential effects on phosphoinositide kinases.