Security and dependability are crucial for designing trustworthy systems. The approach “security as an add-on” is not satisfactory, yet the integration of security in the development process is still an open problem. Especially, a common framework for specifying dependability and security is very much needed. There are many pressing challenges however; here, we address some of them. Firstly, security for dependable systems is a broad concept and traditional view of security, e.g., in terms of confidentiality, integrity and availability, does not suffice. Secondly, a clear definition of security in the dependability context is not agreed upon. Thirdly, security attacks cannot be modeled as a stochastic process, because the adversary’s strategy is often carefully planned. In this chapter, we explore these challenges and provide some directions toward their solutions.