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This thesis is divided into eight chapters as follows: Chapter 1: Chaos is first reviewed and basic features of chaos are introduced. Chaos in electronic circuits is presented. The differences between chaotic communication systems and traditional communication systems are discussed. The basic advantages of using chaotic signals in communication systems are given. Chapter 2: the basic methods of synchronisation in chaotic communication systems are discussed. A survey of analogue chaotic communication systems, showing the advantages and the disadvantages of these systems, is introduced. A new analogue chaotic communication system called the multi-channel chaotic communication system is developed. A survey of different methods of chaos shift keying (CSK) is introduced. The one generator chaos shift keying is presented. Chapter 3: A new method for real time implementation of chaotic systems is developed. The description of the method is presented. The real time implementations of several chaotic generators using the developed method are presented. The implementation of the multi-channel chaotic communication system in real time using the developed method is presented. Chapter 4: A new J-band chaotic generator for radar and microwave communication systems is presented. Theoretical analysis and pratical design of the chaotic generator are given. The design of the receiver part of the chaotic radar and microwave communication systems is presented. The effects of the channel attenuation and channel delay are given. Chapter 5: We start with a survey of classical encryption algorithms and a background of chaotic encryption algorithms. New algorithms for encrypting and decrypting voice, text and image files using chaotic systems are presented. Several examples for encrypting text and image files are given. Comparison between new algorithms and classical encryption algorithms is given. Chapter 6: We start with a general description of the system security and a background of attacking methods of chaotic communication systems. New attacking algorithm to chaotic communication systems is presented. Several results of the algorithm in attacking continuous and discrete chaotic communication systems are given. Chapter 7: New methods for counter measures to the chaotic attacking algorithm are presented. A method for counter counter measures of the chaotic attacker is presented. Chapter 8: The conclusion and the future work are presented.