Salvia sclarea L. is an important industrial crop, valued for its herbal-aromatic properties and high quality essential oils, that is used in food, pharmaceuticals and cosmetics. In this study, carried out from 2009 to 2010, the morphological and production characteristics and essential oil content and composition of three Sicilian populations were studied. In particular, the composition of essential oils extracted from primary and secondary inflorescences using steam distillation was assessed. Morphological, production and qualitative data from the three populations were subjected to analysis of variance and cluster analysis. Regarding the quality of the oils, only the most prevalent compounds were taken into consideration in this study. The three populations were linalyl acetate/linalool chemotypes. Highly significant variations were found for the effective local population and inflorescence type in the composition of the essential oil principal components. In particular, the primary inflorescences were found to be accumulation sites favoured by monoterpenes, and secondary inflorescences were favoured by sesquiterpenes and sclareol. Populations “S. Stefano Quisquina” and “Alcara Li Fusi” performed best on a morphological and production level, whereas populations “Prizzi”and “Alcara Li Fusi” performed best in terms of quality. Population “S. Stefano Quisquina” produced high levels of sclareol. Biotype selection from within the populations should be based on both morphological, production and quality analyses.