For simulated moving bed (SMB) systems with significant mass-transfer effects, a model-based design method, which requires accurate mass-transfer parameters, was developed previously (Wu et al. Ind. Eng. Chem. Res. 1998, 37, 4023). An extended standing wave design method is developed in this study and tested using computer simulations and pilot-scale SMB experiments for the separation of phenylalanine (phe) and tryptophan (trp). In this method, propagation speeds of impurity waves are estimated from the effluent histories of SMB runs based on a design that does not consider mass-transfer effects. According to the impurity wave speeds, zone flow rates and switching time are modified to counterbalance the mass-transfer effects. The values of the individual mass-transfer parameters are not needed. High-purity (96-99%) and high-yield (96-99%) products are obtained. This method is simpler than the model-based design method and can be applied when mass-transfer parameters are either unknown or inaccurate.