Copper-exchanged zeolite chabazite (Cu-SSZ-13) was recently commercialized for the selective catalytic reduction of NO X with ammonia in vehicle emissions as it exhibits superior reaction performance and stability compared to all other catalysts, notably Cu-ZSM-5. Herein, the 3D distributions of Cu as well as framework elements (Al, O, Si) in both fresh and aged Cu-SSZ-13 and Cu-ZSM-5 are determined with nanometer resolution using atom probe tomography (APT), and correlated with catalytic activity and other characterizations. Both fresh catalysts contain a heterogeneous Cu distribution, which is only identified due to the single atom sensitivity of APT. After the industry standard 135,000 mile simulation, Cu-SSZ-13 shows Cu and Al clustering, whereas Cu-ZSM-5 is characterized by severe Cu and Al aggregation into a copper aluminate phase (CuAl2O4 spinel). The application of APT as a sensitive and local characterization method provides identification of nanometer scale heterogeneities that lead to catalytic activity and material deactivation.