Illegal trafficking of pharmaceutical products by criminal organisations is a global threat for public health. Drugs for erectile dysfunction such as phosphodiesterase type 5 inhibitors are the most commonly counterfeited medicines in Europe. The search of possible toxic chemical substances in seized products is needed to provide early warning for public health. Furthermore, the elemental profile of the seized products can be useful in criminal investigations. For the first time an ion beam analysis (IBA) procedure to characterise authentic Viagra® tablets and sildenafil-based illegal products is described. Moreover, results are compared with the ones obtained by instrumental neutron activation analysis (INAA) on authentic Viagra® tablets in two reactors. IBA results showed that a combination of particle-induced X-ray emission (PIXE) and secondary ion mass spectrometry using primary ions with energies in the range of several MeV (MeV-SIMS) is a powerful tool to characterise different products in a straightforward manner, allowing discrimination between legal and illegal products. INAA allowed accurate elemental quantification and also showed a great potential for the future implementation of an inter-laboratory classification system.