The multiobjective optimization of continuous countercurrent chromatography separation units, such as simulated moving bed (SMB) and Varicol, is considered. The Varicol system is based on a nonsynchronous shift of the inlet and outlet ports instead of the synchronous one used in the SMB technology. The optimization problem is complicated by the relative large number of decision variables, including continuous variables, such as flow rates and lengths, as well as discontinuous ones, such as column number and configuration. It is also important to reformulate the optimization problem as multiobjective, since the factors affecting the cost of a given separation process are multiple and often in conflict with each other. A typical example is simultaneous maximization of the productivity of the process and the purity of the corresponding products. A new optimization procedure based on a genetic algorithm allows handling these complex optimization problems. An existing literature chiral separation model was used to illustrate the potential of this optimization procedure. This work also offered a unique opportunity to compare the optimal separation performance achievable with the SMB and Varicol technologies.