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Agent technology is a novel approach for the development of distributed systems. In particular, mobile agents can provide much greater flexibility and robustness than the traditional distributed system methodologies since they provide mobility from platform to platform. Thus, they form a vast area of research. One key problem faced by the mobile agent systems is security. A migrating agent can face many threats while migrating to a host/ agent platform. Similarly the platform can be maliciously affected by an agent. A number of different approaches have been suggested in the literature to deal with security of mobile agents. In this thesis, we present an overview of such threats and present an "agent threat model" for mobile agent systems. Based on this model, we survey and evaluate the techniques that provide countermeasures to the mobile agent systems. Based on the techniques surveyed, a state-of-the-art is evaluated and the security of certain mobile agent systems is discussed. The thesis presents a proposed framework to provide mobile agent system security from both malicious mobile agents and platform. The idea is to provide a solution to the requirement of a security framework that provides security as a combination of components based on techniques for mobile agent system security and protection. The proposed framework is comprised of various components that are studied in the light of operation scenarios. An implementation of the system is discussed and the evaluation of the proposed framework as well as a comparison with the state-of-the-art mobile agent systems is provided to highlight the strengths and weaknesses.