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Long-term electrocardiogram (ECG) monitoring, as a representative application of cyber-physical systems, facilitates the early detection of arrhythmia. A considerable number of previous studies has explored monitoring techniques and the automated analysis of sensing data. However, ensuring patient privacy or confidentiality has not been a primary concern in ECG monitoring. First, we propose an intelligent heart monitoring system, which involves a patient-worn ECG sensor (e.g., a smartphone) and a remote monitoring station, as well as a decision support server that interconnects these components. The decision support server analyzes the heart activity, using the Pan–Tompkins algorithm to detect heartbeats and a decision tree to classify them. Our system protects sensing data and user privacy, which is an essential attribute of dependability, by adopting signal scrambling and anonymous identity schemes. We also employ a public key cryptosystem to enable secure communication between the entities. Simulations using data from the MIT-BIH arrhythmia database demonstrate that our system achieves a 95.74% success rate in heartbeat detection and almost a 96.63% accuracy in heartbeat classification, while successfully preserving privacy and securing communications among the involved entities.