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While interconnected systems proliferate in nowadays computing and communications technology there are few reports investigating their security. In this paper, new efficient models are developed and evaluated for analyzing the security-related behavior of computing architectures and networks comprising complex interconnected communication systems adapted towards a generalized analysis. These models, based on Markov processes, allow calculation of critical security factors, related to intrusion detection, of such interconnected systems components and the evaluation of the associated security mechanisms. Although, at this step two interconnected systems are analyzed, the systematic model introduced allows for a generalized model of N interconnected systems. We herein show the principles of such an analysis. Security parameters calculation and Security mechanisms evaluation may support the risk analysis and the decision making process in resolving the trade-offs between security and quality of service characteristics corresponding to the complex interconnected computing and communication systems.