Automated parallel synthesis as tool to increase productivity in chemical synthesis is well-established. However, even more time-consuming than the synthesis process is the following purification of the resulting crude products. To enhance efficiency of the lead optimization process at Bayer CropScience, a high-throughput HPLC/MS-laboratory for the purification of up to 48 crude products per day in the range of 200-400 mg each in one injection per sample has been set up. The use of Covaris technology for HPLC sample preparation, automated aliquotation during fractionation, and a novel evaporation process by combination with freeze-drying are new key technologies applied successfully for the first time in this purification unit facilitating to achieve the targeted efficiency. The whole process is supported by a specially designed IT-landscape covering each step of the workflow. Both the technical instruments used within the laboratory and the workflow and IT platform are described in this article.