IQGAP1 is a scaffolding protein involved in multiple fundamental cellular activities, including transcription, cell-cell attachment and regulation of the cytoskeleton. In order to function in these pathways, IQGAP1 associates with numerous proteins such as actin, calmodulin, E-cadherin, -catenin, CLIP-170 and components of the mitogen-activated protein kinase pathway. Moreover, IQGAP1 binds to active Cdc42 and Rac1, but not RhoA or Ras. Here we show that IQGAP1 also binds to the small GTPase Rap1. In vitro analysis demonstrates a direct interaction between Rap1 and IQGAP1, which is augmented by activation (GTP-loading) of Rap1. Cdc42 does not modulate the interaction between Rap1 and IQGAP1. In contrast, the association is eliminated by calmodulin, both in the absence and presence of Ca2+. The binding of Rap1 to a point mutant IQGAP1 construct that is unable to interact with calmodulin is 2.5 fold more than to wild type IQGAP1. Consistent with these findings, Rap1 binds to the IQ region of IQGAP1. Confocal microscopy demonstrates that Rap1 and IQGAP1 co-localize at the periphery of human epithelial cells, but not in the cytoplasm. The interaction has functional sequelae. Overexpression of IQGAP1 substantially reduces adhesion-mediated activation of Rap1. In addition, Rap1 activation by cAMP is attenuated in cells that overexpress IQGAP1 and enhanced in cells lacking IQGAP1. These findings reveal that the interaction of IQGAP1 with Rap1 differs in several respects from its interaction with other small GTPases. Furthermore, our data suggest that IQGAP1 may link the calmodulin and Rap1 signalling pathways.