A method and apparatus for controlling an optimization of handover procedures between universal terrestrial radio access (UTRA) release 6 (R6) cells and UTRA release 7 (R7) cells are disclosed. When a wireless transmit/receive unit (WTRU) is moving between an R6 cell and an R7 cell, or between R7 cells, a handover is initiated from a source Node-B to a target Node-B. In the R7 cell, the enhanced medium access control (MAC) functionality including flexible radio link control (RLC) protocol data unit (PDU) size and high speed MAC (MAC-hs) segmentation and multiplexing of different priority queues are supported. After the handover, a MAC layer and/or an RLC layer are reconfigured or reset based on functionality supported by the target Node-B.