The last five years have witnessed the successful application of game theory in reasoning about complex security problems [Basilico et al. 2009; Korzhyk et al. 2010; Dickerson et al. 2010; Jakob et al. 2010; Paruchuri et al. 2008; Pita et al. 2009; Pita et al. 2010; Kiekintveld et al. 2009; Jain et al. 2010]. Stackelberg games have been widely used to model patrolling or monitoring problems in security. In a Stackelberg security game, the defender commits to a strategy and the adversary makes its decision with knowledge of the leader’s commitment. Two systems applying Stackelberg game models to assist with randomized resource allocation decisions are currently in use by the Los Angeles International Airport (LAX) [Pita et al. 2008] and the Federal Air Marshals Service (FAMS) [Tsai et al. 2009]. Two new applications called GUARDS (Game-theoretic Unpredictable and Randomly Deployed Security) [Pita et al. 2011] and PROTECT (Port Resilience Operational / Tactical Enforcement to Combat Terrorism) are under development for the Transportation Security Administration (TSA) and the United States Coast Guard respectively. Both are based on Stackelberg games. In contrast with previous applications at LAX and FAMS, which focused on one-off tailored applications and one security activity (e.g., canine patrol, checkpoints, or covering flights) per application, both GUARDS and PROTECT face new challenging issues due to the potential large scale deployment. This includes reasoning about hundreds of heterogeneous security activities, reasoning over diverse potential threats, and developing a system designed for hundreds of end-users. In this article we will highlight several of the main issues that have arisen. We begin with an overview of the new applications and then discuss these issues in turn.