The inherent structural and physiological complexity of congenital heart disease lends itself strongly to simulation. Complex hemodynamic and structural problems unique to congenital heart disease may be difficult to understand and the response to therapy or intervention uncertain. Methodologies borrowed from engineering, computing and mathematical sciences can be applied to such problems and used to inform clinical decisions. Therapy thus informed by modeling experiments has the potential to contribute significantly to improved clinical outcomes. This field remains in its infancy, and will only become used routinely if validation of current methods is carried out in the clinical setting.