As wireless networks continue to flourish worldwide and play an increasingly prominent role, it has become crucial to provide effective solutions to the inherent security issues associated with a wireless transmission medium. Unlike traditional solutions, which usually handle security at the application layer, the primary concern of this thesis is to analyze and develop solutions based on coding techniques at the physical layer. First, an information-theoretically secure communication protocol for quasi-static fading channels was developed and its performance with respect to theoretical limits was analyzed. A key element of the protocol is a reconciliation scheme for secret-key agreement based on low-density parity-check codes, which is specifically designed to operate on non-binary random variables and offers high reconciliation efficiency. Second, the fundamental trade-offs between cooperation and security were analyzed by investigating the transmission of confidential messages to cooperative relays. This information-theoretic study highlighted the importance of jamming as a means to increase secrecy and confirmed the importance of carefully chosen relaying strategies. Third, other applications of physical-layer security were investigated. Specifically, the use of secret-key agreement techniques for alternative cryptographic purposes was analyzed, and a framework for the design of practical information-theoretic commitment protocols over noisy channels was proposed. Finally, the benefit of using physical-layer coding techniques beyond the physical layer was illustrated by studying security issues in client-server networks. A coding scheme exploiting packet losses at the network layer was proposed to ensure reliable communication between clients and servers and security against colluding attackers.