Calcineurin (CN), the Ca(2+)/calmodulin (CaM)-dependant protein phosphatase, is an integral enzyme involved in activation of T cells. It is also the target of various inhibitors such as cyclosporine A (CsA) and FK506 both of which have been widely used as immunosuppressants. We show that the novel CN inhibitor, quercetin (QC), associates with CN both in vitro and in Jurkat cells, and that it causes non-competitive inhibition of phosphatase activity. Unlike CsA and FK506, QC does not require a matchmaker protein for CN inhibition. It acts directly on the catalytic domain and its inhibitory effect was increased by the presence of CNB. Using semi-quantitative and real-time RT-PCR, we show that QC inhibits IL-2 gene expression in activated Jurkat cells. The physiological inhibitory activity of QC together with its hypotoxicity suggests that it may be an effective immunosuppressant.