The huge number of containers daily involved in the global transportation system opens important logistic and security issues. The matter of improving the management of goods in the harbor and the serious vulnerability problem of containers are relevant topics in the commercial supply chain. In fact, both can be easily exploited as carriers for illegal and dangerous items. In this paper, we focus on the security of commercial containers starting with the analysis of the most common technologies presently used in the field. Then, we concentrate on the research carried out by the Joint Research Centre (JRC) of the European Commission in the field of supply chain security. In particular, we discuss in-depth our innovative active RFID-based sealing systems designed at the JRC, giving a detailed technological description of its working logic and main features. Experimental results of the laboratory tests are presented, in order to show the performance of the system and its capabilities in improving security in commercial transportation systems.