Design equations were derived from standing wave analysis for continuous moving bed (CMB) and simulated moving bed (SMB) systems with nonlinear isotherms. Simple wave solutions and hodograph plots from batch elution experiments can be used to derive the optimal operation conditions for SMB systems without mass-transfer effects. The design equations are tested with results from computer simulations and experimental data from two pilot-scale SMB units for the separation of fructose from glucose. Batch equilibrium tests of single component and binary solutions are used to estimate adsorption isotherm parameters. Overall mass-transfer and axial dispersion coefficients are estimated from eight sets of pulse, frontal and elution data at different concentrations and flow rates. The isotherm and mass-transfer parameters are used in the standing wave analysis to determine the zone flow rates and switching times for the two SMB units. Experimental column profiles, product purities, and product concentrations agree closely with simulation results. This method gives robust operation conditions for SMB systems with nonlinear isotherms, and optimal cycle time and zone flow rates for nonlinear systems without mass-transfer effects can be determined from the standing wave analysis.