This disclosure describes techniques for programming stimulation therapy programs according to therapy targets (e.g., symptoms or areas of pain) in a patient to which they are applied. Several programs can be programmed for each therapy target, stored on an implantable medical device, and retrieved later by a programmer to modify, edit, delete, create, and/or select a therapy program for each of the therapy targets. Each therapy target is independent from the other therapy targets, and a user can select or change a program under one therapy target without affecting programs under the other therapy targets. During programming, a user can specify parameters for each program applicable to only that program, and can specify parameters for each therapy target applicable to every program associated with that therapy target. The organization of programs into slots and the selection of a program in each slot may be manual or automated.