Human Rap1GAP, the GTPase-activating protein (GAP) for the small GTPase Rap1, was recombinantly expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. Crystals were obtained using PEG 3350 as a precipitating agent and belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 170.7, b = 224.5, c = 48.7 A. A complete data set was collected to 2.9 A resolution at 100 K using synchrotron radiation. The structure may reveal features of the unique reaction mechanism of Rap1GAP.