We have previously reported the design of a portable 109Cd x-ray fluorescence (XRF) system to measure iron levels in the skin of patients with either iron overload disease, such as thalassemia, or iron deficiency disease, such as anemia. In phantom studies, the system was found to have a detection limit of 1.35 μg Fe per g of tissue for a dose of 1.1 mSv. However, the system must provide accurate as well as precise measurements of iron levels in the skin in order to be suitable for human studies. The accuracy of the system has been explored using several methods. First, the iron concentrations of ten pigskin samples were assessed using both the portable XRF system and ICP-MS, and the results were compared. Overall, it was found that XRF and ICP-MS reported average values for iron in skin that were comparable to within uncertainties. The mean difference between the two methodologies was not significant, 2.5 ± 4.6 μg Fe per g. On this basis, the system could be considered accurate. However, ICP-MS measurements reported a wider range of values than XRF, with two individual samples having ICP-MS results that were significantly elevated (p < 0.05) compared to XRF. Synchrotron μXRF maps of iron levels in pigskin were acquired on the BioXAS beam line of the Canadian Light Source. The μXRF maps indicated two important features in the distribution of iron in pigskin. First, there were small areas of high iron concentration in the pigskin samples, that were predominantly located in the dermis and hypodermis at depths greater than 0.5 mm. Monte Carlo modelling using the EGS 5 code determined that if these iron ‘hot spots’ were located towards the back of the skin at depths greater than 0.5 mm, they would not be observed by XRF, but would be measured by ICP-MS. These results support a hypothesis that iron levels in the two samples that reported significantly elevated ICP-MS results compared to XRF may have had small blood vessels at the back of the skin. Second, the synchrotron μXRF maps also showed a narrow (approximately 100μm thick) layer of elevated iron at the surface of the skin. Monte Carlo models determined that, as expected, the XRF system was most sensitive to these skin layers. However, the simulations found that the XRF system, when calibrated against homogenous water-based phantoms, was found to accurately measure average iron levels in the skin of normal pigs despite the greater sensitivity to the surface layer. The Monte Carlo results further indicated that with highly elevated skin surface iron levels, the XRF system would not provide a good estimate of average skin iron levels. The XRF estimate could, with correction factors, provide a good estimate of the iron levels in the surface layers of skin. There is limited data on iron distribution in skin, especially under conditions of disease. If iron levels are elevated at the skin surface by diseases including thalassemia and hemochromatosis, this XRF device may prove to be an accurate clinical tool. However, further data are required on skin iron distributions in healthy and iron overload disease before this system can be verified to provide accurate measurements.