In this paper we identify some of the particular challenges that are encountered when trying to secure cyber-physical systems. We describe three of our current activities: the architecture of a system for monitoring cyber-physical systems; a new approach to modelling dependencies in such systems which leads to a measurement of the security of the system – interpreted as the least effort that an attacker has to expend to compromise the operation; and an approach to optimising the diversity of products used in a system with a view to slowing the propagation of malware. We conclude by discussing how these different threads of work contribute to meeting the challenges and identify possible avenues for future development, as well as providing some pointers to other work.