Recent developments in combinatorial molecular design using virtual screening methods are summarised. These include similarity-based compound clustering techniques, structure-based docking and scoring, and fragment-based de novo design. Three major trends have been identified: i) the design of small target-focused compound libraries yielding activity-enriched sets of molecules; ii) advanced prediction methods for "drug-like" molecular properties complement activity predictions in the library design process, forming a multi-dimensional objective function; iii) "cherry picking" of selected products is increasingly used in lead generation and optimisation compared to purely educt-driven library design methods aiming at maximising structural diversity.