A method implemented at a wireless transmit/receive unit, WTRU, for handling carrier aggregation, comprising: establishing a connection with a primary cell, PCell; configuring the WTRU with a secondary cell, SCell; receiving an activation/deactivation medium access control, MAC, control element, CE, comprising fields for signaling activation/deactivation states for multiple SCells; determining the activation/deactivation state for the SCell for which the WTRU is configured using an identity of the SCell as an index to the activation/deactivation MAC CE; activating or deactivating the SCell based on the determined activation/deactivation state; triggering a power headroom report, PHR, responsive to activation of the SCell and on a condition that the SCell is configured for uplink transmission; and generating a MAC protocol data unit, PDU, having a MAC PHR CE on condition that the PHR is pending in a subframe for which the WTRU has uplink resources allocated for at least one new transmission on at least one serving cell and taking into account a relative priority of the MAC PHR CE within an ordered group of MAC CEs, wherein the MAC PHR CE includes respective power headroom values for the concerned SCell, the PCell and one or more other SCells configured for uplink transmission and activated in the subframe, and wherein each of the power headroom values is a value based on transmitting on one or more physical uplink channels in the subframe of the at least one serving cell or a value derived by the WTRU based on transmitting on one or more physical uplink channels of the at least one serving cell although no transmission is performed. establishing a connection with a primary cell, PCell; configuring the WTRU with a secondary cell, SCell; receiving an activation/deactivation medium access control, MAC, control element, CE, comprising fields for signaling activation/deactivation states for multiple SCells; determining the activation/deactivation state for the SCell for which the WTRU is configured using an identity of the SCell as an index to the activation/deactivation MAC CE; activating or deactivating the SCell based on the determined activation/deactivation state; triggering a power headroom report, PHR, responsive to activation of the SCell and on a condition that the SCell is configured for uplink transmission; and generating a MAC protocol data unit, PDU, having a MAC PHR CE on condition that the PHR is pending in a subframe for which the WTRU has uplink resources allocated for at least one new transmission on at least one serving cell and taking into account a relative priority of the MAC PHR CE within an ordered group of MAC CEs, wherein the MAC PHR CE includes respective power headroom values for the concerned SCell, the PCell and one or more other SCells configured for uplink transmission and activated in the subframe, and wherein each of the power headroom values is a value based on transmitting on one or more physical uplink channels in the subframe of the at least one serving cell or a value derived by the WTRU based on transmitting on one or more physical uplink channels of the at least one serving cell although no transmission is performed.