Motor program theory has provided physical therapists with one approach to understanding how the brain controls movement. Analogous with computer programs that specify the operations of computer hardware, motor programs are thought to contain commands for muscles that allow movements to occur without the need for continuous peripheral feedback. A review of the physical therapy literature reveals many instances in which motor program theory has been used as a theoretical framework for clinical practice. Yet despite the contribution programming theory has made to the advancement of movement science, the motor program construct is currently under considerable threat. Keele's (1968) original definition no longer seems tenable, given the problems of program storage, motor equivalence, movement flexibility, and context-conditioned variability. The finding that researchers from different disciplines define the motor program in a variety of ways adds difficulty to the task of evaluating the efficacy of the model. A critical appraisal of programming theory and its use in physical therapy suggests that clinicians need to reconsider the usefulness of the motor program model as a basis for movement rehabilitation following brain damage and musculoskeletal disorders.