Enhancements are provided for the radio link control (RLC) protocol in wireless communication systems where variable RLC packet data unit (PDU) size is allowed. When flexible RLC PDU sizes are configured by upper layers, radio network controller (RNC)/Node B flow control, RLC flow control, status reporting and polling mechanisms are configured to use byte count based metrics in order to prevent possible buffer underflows in the Node B and buffer overflows in the RNC. The enhancements proposed herein for the RLC apply to both uplink and downlink communications.