Latest Fusion energy experiments envisage a quasi-continuous operation regime. In consequence, the largest experimental devices, currently in development, specify high-availability (HA) requirements for the whole plant infrastructure. Highly available systems operate seamlessly in the case of component failure, ensuring safety of equipment, people, environment and investment. Control and Data Acquisition (C&DA) systems for Fusion diagnostics are considered mission-critical and require high degrees of availability. IPFN developed a C&DA system for fast control of advanced Fusion devices, targeting HA. The hardware platform is based on in-house developed Advanced Telecommunication Computing Architecture (ATCA) instrumentation modules–digitizing and data switch blades using PCI Express (PCIe) over the ATCA backplane Fabric Channel Interface, connecting to an external PCIe host computer. At the hardware management level, the system architecture takes advantage of ATCA’s HA characteristics, such as its redundant hardware components, redundant backplane topologies and Field Replaceable Unit (FRU) “Hot Swap”. At the software level, PCIe supports “Hot Plug” graceful device insertion and removal. The implementation of PCIe Hot Plug for the ATCA form-factor is one of the major tasks involved and a solution for such implementation was also developed. The paper describes how IPFN C&DA system can be setup to take advantage of both ATCA and PCIe features to perform with the desired degree of availability, by implementing fail-over mechanisms based on the use of redundancy, thus being suitable for advanced C&DA systems in Fusion.