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The biocompatibility and nanoscale features of Molecular Communication (MC) make this paradigm, based on molecules and chemical reactions, an enabler for communication theory applications in the healthcare at its biological level (e.g., bimolecular disease detection/monitoring and intelligent drug delivery). However, the adoption of MC-based innovative solutions into privacy and security-sensitive areas is opening new challenges for this research field. Despite fundamentals of information theory applied to MC have been established in the last decade, research work on security in MC systems is still limited. In contrast to previous literature focused on challenges, and potential roadmaps to secure MC, this paper presents the preliminary elements of a systematic approach to quantifying information security as it propagates through an MC link. In particular, a closed-form mathematical expression for the secrecy capacity of an MC system based on free molecule diffusion is provided. Numerical results highlight the dependence of the secrecy capacity on the average thermodynamic transmit power, the eavesdropper’s distance, the transmitted signal bandwidth, and the receiver radius. In addition, the concept of secure distance in an MC system is introduced and investigated for two different techniques of signal detection, i.e., based on energy and amplitude. The secrecy capacity can be used to determine how much secure information (bit/sec/Hz) can be exchanged and within which operative range, while the secure distance can be used to set the transmit power to obtain a secure channel at a given distance. We envision these metrics will be of utmost importance for a future design framework tailored to MC systems and their practical applications.