Sixty-five samples of propolis were collected from eleven regions of Cuba; methanolic extracts of propolis were prepared from all samples, and a classification method was developed using a combination of NMR, HPLC-PDA, and HPLC-ESI/MS techniques. The analysis of (1)H and (13)C NMR spectra and chromatographic profiles of all propolis extracts allowed the definition of three main types of Cuban propolis directly related to their secondary metabolite classes: brown Cuban propolis (BCP), rich in polyisoprenylated benzophenones, red Cuban propolis (RCP), containing isoflavonoids as the main constituents, and yellow Cuban propolis (YCP), probably with aliphatic compounds. Subsequently, the principal compounds of the brown and red types were characterized by HPLC-ESI/MS analysis. Instrumental techniques used are complementary; NMR was shown to be a quick and informative tool for the rapid analysis of crude propolis polar extracts and allowed the identification of the main class of secondary metabolites, while LC-PDA and LC-MS techniques were useful tools for qualitative and quantitative analysis of marker compounds of Cuban propolis.