The utility of ion beam analysis (IBA) techniques to quantitatively determine impurities in carbon nanotubes (CNTs) over a wide range of atomic numbers is demonstrated. Such techniques have not previously been used to monitor impurities and their effects in this unique material. Despite the difficulty in mounting the samples (which generally are formed into a powdery aggregate rather in a thin film), it is shown that reliable and accurate measurements of impurity concentrations can be achieved. Particle-induced X-ray emission (PIXE) and elastic recoil detection (ERD) analyses were used to characterize both metallic and very light (e.g., hydrogen) impurities in CNTs. This paper reports the first direct measurement of hydrogen in CNTs using an IBA technique. This is significant because CNTs are being actively investigated for hydrogen storage technology for energy applications.