The production and sale of counterfeit and substandard pharmaceutical products, such as essential medicines, is an important global public health problem. We describe a chemometric passport-based approach to improve the security of the pharmaceutical supply chain. Our method is based on applying nuclear quadrupole resonance (NQR) spectroscopy to authenticate the contents of medicine packets. NQR is a non-invasive, non-destructive, and quantitative radio frequency (RF) spectroscopic technique. It is sensitive to subtle features of the solid-state chemical environment and thus generates unique chemical fingerprints that are intrinsically difficult to replicate. We describe several advanced NQR techniques, including two-dimensional measurements, polarization enhancement, and spin density imaging, that further improve the security of our authentication approach. We also present experimental results that confirm the specificity and sensitivity of NQR and its ability to detect counterfeit medicines.