Abstract: The effects produced by swift heavy ions in the martensitic (18R) and austenitic phase (beta) of Cu based shape memory alloys were characterized. Single crystal samples with a surface normal close to [210](18R) and [001](beta) were irradiated with 200 MeV of Kr(15+), 230 MeV of Xe(15+), 350 and 600 MeV of Au(26+) and Au(29+). Changes in the microstructure were studied with transmission electron microscopy (TEM) and high resolution transmission electron microscopy (HRTEM). It was found that swift heavy ion irradiation induced nanometer sized defects in the 18R martensitic phase. In contrast, a hexagonal close-packed phase formed on the irradiated surface of beta phase samples. HRTEM images of the nanometer sized defects observed in the 18R martensitic phase were compared with computer simulated images in order to interpret the origin of the observed contrast. The best agreement was obtained when the defects were assumed to consist of local composition modulations.