Heterogeneous diffusion in different regions of a fractured granodiorite from Japan has been observed and measured through the use of X-ray absorption imaging. These regions include gouge-filled fractures, recrystallized fracture-filling material and hydrothermally altered matrix. With the X-ray absorption imaging technique, porosity, relative concentration, and relative mass of an iodine tracer were imaged in two dimensions with a sub-millimeter pixel size. Because portions of the samples analyzed have relatively low porosity values, imaging errors can potentially impact the results. For this reason, efforts were made to better understand and quantify this error. Based on the X-ray data, pore diffusion coefficients (Dp) for the different regions were estimated assuming a single diffusion rate and a lognormal multirate distribution of Dp. Results show Dp for the gouge-filled fractures are over an order of magnitude greater than those of the recrystallized fracture-filling material, which in turn is approximately two times greater than those for the altered matrix. The recrystallized fracture-filling material was found to exhibit the greatest degree of variability. The results of these experiments also provide evidence that diffusion from advective zones in fractures through the gouge-filled fractures and recrystallized fracture-filling material could increase the pore space available for matrix diffusion. This evidence is important for understanding the performance of potential nuclear waste repositories in crystalline rocks as diffusion is thought to be an important retardation mechanism for radionuclides.