Secure communication over large-scale decentralized wireless networks is an extremely challenging task due to the cost and difficulty in establishing secret keys among all the nodes in a distributed manner. For this reason, the notion of physical layer security has recently drawn significant attention, which may assist with key exchange and provide an additional layer of protection in such networks. In this paper, we investigate how the physical layer security constraints affect the network throughput. We consider a random network in which the legitimate and eavesdropper nodes are located according to independent Poisson point processes. We introduce a new metric “secrecy transmission capacity” to characterize the network throughput in terms of the area spectral efficiency of secure transmissions, subject to constraints on both the quality of service and the level of security. This capacity framework allows us to quantitatively study the throughput cost of physical layer security constraints. We observe 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.