Ciphering control and synchronization for both U-plane data and C-plane signaling messages in a wireless communication network are disclosed. Ciphering entities are located in a wireless transmit/receive unit (WTRU) and a network. The ciphering entities of the WTRU and the network perform ciphering control and ciphering parameter synchronization. The ciphering may be performed with a packet data convergence protocol (PDCP) layer sequence number (SN) for user plane data, a non-access stratum SN, a radio resource control SN, or an encryption SN for a control plane message. Alternatively, the ciphering control and ciphering parameter synchronization may be performed by PDCP entities of the WTRU and the network. For ciphering parameter synchronization, HFN and SN synchronization and counter check procedures are performed by the WTRU and the network based on a synchronization command message, sequence number window information, or a counter check message exchanged between the WTRU and the network.