Atom-probe tomography (APT) and secondary ion mass spectrometry (SIMS) provide complementary in situ element and isotope data in minerals such as zircon. SIMS measures isotope ratios and trace elements from 1-20 μm spots with excellent accuracy and precision. APT identifies mass/ charge and three-dimensional position of individual atoms (±0.3 nm) in 100 nm-scale samples, volumes up to one million times smaller than SIMS. APT data provide unique information for understanding element and isotope distribution; crystallization and thermal history; and mechanisms of mineral reaction and exchange. This atomistic view enables evaluation of the fidelity of geochemical data for zircon because it provides new understanding of radiation damage, and can test for intracrystalline element mobility. Nano-geochronology is one application of APT in which Pb isotope ratios from sub-micrometer domains of zircon provide model ages of crystallization and identify later magmatic and metamorphic reheating.Based on SEM imaging and SIMS analysis, 11 needle-shaped specimens ~100 nm in diameter were sampled from one Archean and two Hadean zircons by focused ion-beam milling and analyzed with APT. The three-dimensional distribution of Pb and nominally incompatible elements (Y, REEs) differs at the atomic scale in each zircon. Zircon JH4.0 (4.007 Ga, Jack Hills, Western Australia) is homogeneous in Pb, Y, and REEs. In contrast, Pb and Y and REEs are clustered in sub-equant ~10 nm diameter domains, spaced 10-40 nm apart in zircons ARG2.5 (2.542 Ga, Grouse Creek Mountains, Utah) and JH4.4 (4.374 Ga, Jack Hills). Most clusters are flattened parallel to (100) or (010). U and Th are not collocated with Pb in clusters and appear to be homogeneously distributed in all three zircons. The analyzed domains experienced 4 to 8 × 10 15 α-decay events/mg due to U and Th decay and yet all zircons yield U-Pb ages by SIMS that are better than 97% concordant, consistent with annealing of most radiation damage. The 207 Pb/ 206 Pb ratios for the 100 nm-scale specimens measured by APT average 0.17 for ARG2.5, 0.42 for the JH4.0, and 0.52 for JH4.4. These ratios are less precise (±10-18% 2σ) due to the ultra-small sample size, but in excellent agreement with values measured by SIMS (0.1684, 0.4269, and 0.5472, respectively) and the crystallization ages of the zircons. Thus Pb in these clusters is radiogenic, but unsupported, meaning that the Pb is not spatially associated with its parent isotopes of U and Th. For the domain outside of clusters in JH4.4, the 207 Pb/ 206 Pb ratio is 0.3, consistent with the SIMS value of 0.2867 for the zircon overgrowth rim and an age of 3.4 Ga. In ARG2.5, all Pb is concentrated in clusters and there is no detectable Pb remaining outside of the clusters. The Pb-Y-REE-rich clusters and lack of correlation with U in ARG2.5 and JH4.4 are best explained by diffusion of Pb and other elements into ~10 nm amorphous domains formed by α-recoil. Diffusion distances of ~20 nm for these elements in crystalline zircon are consistent with heatin...