The ChemSpaceShuttle toolbox provides a graphical interface allowing for ligand-based design of focused compound libraries by means of linear and non-linear projection techniques and clustering algorithms. The software implements a non-linear encoder network and non-linear partial least squares for the projection of high-dimensional descriptor vectors into a three dimensional space for visualisation. Compound clustering by a self-organising map (SOM) is incorporated. Visualization can facilitate the selection of compounds with desired properties from large compound libraries. Two sample applications are presented: similarity-based compound selection for focused library design, and classification of drugs and nondrugs. A version of ChemSpaceShuttle is freely available at URL: http://gecco.org.chemie.uni-frankfurt.de/gecco.html.