Up to few years ago, FPGAs were not suitable to develop smart sensor systems because of power consumption and programming effort. Modern technologies and programming techniques overcame these limitations. Furthermore thanks to flexible and efficient reconfiguration, FPGAs can be used as configurable wireless sensor nodes and they are very promising in the protection of critical infrastructures. In the recent years, particular emphasis was given to pervasive wireless sensor nodes that enabled the widespread of innovative applications for smartgrid monitoring and mobile cyber-physical infrastructures; although security remains one of the main open challenges to face. In this paper we will analyze all potentialities of adopting FPGAs in protecting Cyber Physical Infrastructures by illustrating with simple scenarios how they can be used to improve security and robustness of heterogeneous networks.