Effective doses for PET and SPECT imaging of molecular imaging agents depend on the radiopharmaceutical, administered activity and the weight of the patient. Effective doses for the accompanying CT scan depend on the CT protocol being used. CT protocols can be designed to produce diagnostic quality images, localization images or attenuation correction data without imaging. In each case, the co-registered molecular imaging examination (PET or SPECT) and the CT study must be acquired without patient movement. For PET/CT, attention to the respiratory phase during the CT study is also of critical importance. In addition to the molecular imaging agents (18)F-FDG and (123)I-MIBG that are frequently used in children, additional PET and SPECT imaging agents may have promise for molecular imaging in children.