Background: In the last decades particular attention has been devoted to packaging materials to obtain the best conditions to store food and to preserve the organoleptic properties.Methods: In the present study samples of tomato sauce collected in different Italian markets and preserved in different packaging materials (glass, tin and multilayer plastic containers) were chemically characterized considering the content of anions (6 species), carotenoids (lycopene, sum of alpha- and beta- carotene), flavonoids (epicatechin and quercetin), metals (41 species), total polyphenols, vitamins (C and B-group), and volatile profile. Different analytical techniques were employed like GC and LC with different detectors (MS and DAD), ICP-MS and ICP-OES. All developed methods were validated and applied to different commercial products collected from local markets. Results: Multivariate statistical tools (Principal Components Analysis – Discriminant Analysis, PCA – DA, Ranking PCA and Partial Least Square – Discriminant Analysis, PLS – DA) were then applied to evaluate the effect played by the different packaging on the chemical profile of the samples. The multivariate strategy adopted allowed to identify markers able to discriminate samples stored in glass, tin or multilayer plastic containers. Conclusion: In both cases, the differences identified between the classes of samples can be ascribed to a double effect: 1) products stored in glass preserve their content in vitamins and other important nutrients or 2) storage in glass could force manufacturers to provide a product of better quality since the product is visible to the final consumer.