This paper studies the throughput of large-scale decentralized wireless networks with physical layer security constraints. In particular, we are interested in the question of how much throughput needs to be sacrificed for achieving a certain level of security. We consider random networks where the legitimate nodes and the eavesdroppers are distributed according to independent two-dimensional Poisson point processes. The transmission capacity framework is used to characterize the area spectral efficiency of secure transmissions with constraints on both the quality of service (QoS) and the level of security. This framework illustrates the dependence of the network throughput on key system parameters, such as the densities of legitimate nodes and eavesdroppers, as well as the QoS and security constraints. One important finding is that the throughput cost of achieving a moderate level of security is quite low, while throughput must be significantly sacrificed to realize a highly secure network. We also study the use of a secrecy guard zone, which is shown to give a significant improvement on the throughput of networks with high security requirements.