We consider the problem of security for unmanned aerial vehicle flight control systems. To provide a concrete setting, we consider the security problem in the context of a helicopter which is compromised by a malicious agent that distorts elevation measurements to the control loop. This is a particular example of the problem of the security of stochastic control systems under erroneous observation measurements caused by malicious sensors within the system. In order to secure the control system, we consider dynamic watermarking, where a private random excitation signal is superimposed onto the control input of the flight control system. An attack detector at the actuator can then check if the reported sensor measurements are appropriately correlated with the private random excitation signal. This is done via two specific statistical tests whose violation signifies an attack. We apply dynamic watermarking technique to a 2-rotor-based 3-DOF helicopter control system test-bed. We demonstrate through both simulation and experimental results the performance of the attack detector on two attack models: a stealth attack, and a random bias injection attack.