We present a Roche tomography reconstruction of the secondary star in the cataclysmic variable AE Aqr. The tomogram reveals several surface inhomogeneities that are due to the presence of large, cool star-spots. In addition to a number of lower latitude spots, the maps also show the presence of a large, high-latitude spot similar to that seen in Doppler images of rapidly rotating isolated stars, and a relative paucity of spots at a latitude of 40°. In total, we estimate that some 18 per cent of the Northern hemisphere of AE Aqr is spotted. We have also applied the entropy landscape technique to determine accurate parameters for the binary system. We obtain optimal masses M1 = 0.74Msolar, M2 = 0.50Msolar, a systemic velocity γ = -63kms-1 and an orbital inclination i = 66°. Given that this is the first study to successfully image star-spots on the secondary star in a cataclysmic variable, we discuss the role that further studies of this kind may play in our understanding of these binaries.