In the event of conventional military attack or invasion by an adversary upon the United States, it is clearly recognized that the US Armed Forces, could legally respond swiftly and decisively to “protect and defend” the nation. However, in the instance of a cyber-attack upon a civilian target in the United States the military’s ability to respond is limited and its role is less clearly defined. The same holds true if the attack is directed against one of the sixteen sectors of US critical infrastructure (CI), such as transportation. In the case of a cyber attack conducted upon transportation CI, failing to prevent, mitigate or respond swiftly could have serious consequences for national and economic security. On the surface, DoD protection of transportation CI against cyber threats may seem to be a convenient solution to a growing problem. On the other hand, DoD involvement in the protection of privately owned infrastructure is wrought with many challenges that are borne out of the scope and nature of the cyber threat as well as the dynamics of the public-private relationship. This paper will explore the cyber threat to US transportation CI, challenges to DoD’s role and offer recommendations to improve DoD’s responsiveness.