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Cloud computing provides outsourcing of resources bringing economic benefits. The outsourcing however does not allow data owners to outsource the responsibility of confidentiality, integrity and access control, as it still is the responsibility of the data owner. As cloud computing is transparent to both the programmers and the users, it induces challenges that were not present in previous forms of distributed computing. Furthermore, cloud computing enables its users to abstract away from low-level configuration such as configuring IP addresses and routers. It creates an illusion that this entire configuration is automated. This illusion is also true for security services, for instance automating security policies and access control in cloud, so that individuals or end-users using the cloud only perform very high-level (business oriented) configuration. This paper investigates the security challenges posed by the transparency of distribution, abstraction of configuration and automation of services by performing a detailed threat analysis of cloud computing across its different deployment scenarios (private, bursting, federation or multi-clouds). This paper also presents a risk inventory which documents the security threats identified in terms of availability, integrity and confidentiality for cloud infrastructures in detail for future security risks. We also propose a methodology for performing security risk assessment for cloud computing architectures presenting some of the initial results.