Non-invasive testing of children with congenital heart disease (CHD) began in the 1950s with the introduction of radionuclide studies to assess shunt fractions, pulmonary blood flow, and ventricular contractile function. Echocardiography and cardiac magnetic resonance imaging have since replaced radionuclide imaging in many of these roles. Concurrently, percutaneous and surgical repairs of complex CHD evolved, creating new roles for radionuclide imaging. In this paper on applications of radionuclide imaging in CHD, we review the multiple mechanisms for myocardial ischemia in CHD. We critically compare optimal radionuclide imaging techniques to other imaging modalities for assessing ischemia in CHD. We present the current role of nuclear imaging for assessing viability and pulmonary blood flow. We highlight the value added by advances in dedicated cardiac SPECT scanners, novel reconstruction software, and cardiac PET in performing low-dose radionuclide imaging in CHD. Finally, we discuss the emerging clinical indications for radionuclide imaging in CHD including coronary flow reserve assessment and evaluation of cardiovascular prosthesis and device infections.