Diffusion of He in zircon and apatite is of fundamental importance in the interpretation of He-loss measurements used in thermochronology. The diffusion of He in zircon is strongly anisotropic, while experimental measurements find He diffusion in apatite to be nearly isotropic. We present the first calculations for He diffusion in Ca5(PO4)3F fluroapatite and re-calculate He diffusivity in zircon, ZrSiO4, in order to make a consistent comparison with the results of the apatite calculations and clarify discrepancies in the literature. Calculated diffusivities for apatite are:D[001](cm2/s)=0.014exp(−84kJmol-1/RT)D[110](cm2/s)=0.024exp(−104kJmol-1/RT)and for zircon:D[001](cm2/s)=0.0039exp(−42kJmol-1/RT)D[100](cm2/s)=0.030exp(−255kJmol-1/RT)He diffusion in ideal zircon is greater than in ideal apatite and anisotropic in both. However, the degree of anisotropy is much more pronounced in zircon. The computational approach allows a comparison of the behavior of the ideal structures (i.e., defect-free) as compared to natural samples that may contain impurities or some level of radiation damage. The calculated diffusivities for the ideal structure are in closer agreement with experimentally determined values for natural apatite than for zircon. The calculations predict that the perfect zircon structure will have high diffusivities due to large uninterrupted “channels” along [001]. However, in natural samples, these channels may be interrupted due to the presence of impurities, e.g., radiogenic Pb, or nanoscale radiation-damage cascades, 5nm in diameter, created by the alpha-decay of incorporated U and Th, thus effectively lowering the diffusivity. The damage microstructure depends on the fluence and thermal history of the sample, and variations in thermal history can lead to variations in the He-loss and the interpreted age and thermal history. Closure temperatures in the ideal structure are extremely low, −35°C for apatite and −150°C for zircon, suggesting the degree of radiation damage plays an important role in attaining closure to He loss.