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Radio frequency identification (RFID) technology is becoming more and more important for tracing and tracking systems. Furthermore, the application of standards, such as EPCglobal, is contributing substantially to diffusing the important concept of Internet of Things. Although, these elements promise enormous benefits, there remain barriers that are limiting a large-scale deployment of these innovative technologies in supply chain management systems. An analysis of the main effects of the use of these technologies on the main processes of a supply chain is useful. This paper attempts to identify key performance indicators (KPIs) to trace the impacts of the combined use of different standards, such as RFID, EPCglobal, and ebXML, on a pharmaceutical supply chain. The current and possible future visions of the pharmaceutical supply chain are described through the AS-IS and TO-BE models. These models are used to perform a first KPI analysis; even if the reported results are still only partial they sketch out the main guidelines identifying the advantages obtainable by adopting an integrated system with B2B messaging and tracing and tracking capabilities in the pharmaceutical supply chain.