Nuclear magnetic resonance (NMR) is a fast and accurate analytical method. Associated with chemometrics, it gradually becomes more important tool for the pharmaceutical industry. In this review studies dealing with the applications of multivariate analysis to NMR spectroscopic profiles were grouped and discussed according to the analytical problem solved. The following topics were covered: authenticity of medicines according to variety, seasonal and geographical differences of herbal plants; quantitative prediction of pharmacologically relevant parameters; production and batches approval; investigation of drug structure modifications; site-specific natural isotope fractionation (SNIF-NMR) fingerprinting for origin and manufacturer tracking and others. Special focus was put on the heparin authenticity by using 1D and 2D NMR measurements. Finally, further research directions have been outlined. Our review has shown that chemometrics plays an important role for the quality control and authenticity of pharmaceutical products and its role will definitely increase in the future. The discussed approaches are recommended to be implemented during development and production process of pharmaceuticals or in quality control laboratories.