There have been several studies that suggest that catalyst metals in carbon nanotubes (CNTs) may pose a health threat. As there are many potential applications of CNTs in medicine, it is important to be able to quantitatively determine the amount of metal catalyst contained in a CNT sample. The relative catalyst content of carbon nanotube samples synthesized via arc-discharge has been determined at various stages of the purification process using X-ray fluorescence (XRF) analysis. Purification was achieved by immersing samples in heated nitric acid. The intensities of the nickel K α X-rays were studied to determine the relative catalyst content in the samples. Scanning electron microscopy (SEM) images of purified nanotubes have been compared to the images of a sample that has been irradiated by 0–15 keV bremsstrahlung in order to determine if the XRF analysis of the nanotubes is in any way destructive. No obvious structural defects were observed as the result of irradiation.