The late effects in children with hypothalamic and thalamic tumors relate to the effects of the tumor on the surrounding brain, the effects of surgery, radiotherapy (RT) and, to a lesser extent, chemotherapy. The clinical manifestations of late effects include endocrinologic dysfunction, neurocognitive sequelae, behavioral problems and second neoplasia. The prevention of late effects is an integral part of current treatment strategies. Early diagnosis, a rational use of surgery, and deferral of RT are the mainstays of the modern treatment in these patients. The improvement of RT techniques and the use of radioprotective compounds may further help spare normal brain tissue. A better understanding of chemotherapy use and the development of newer agents may increase efficacy, reduce side effects and allow deferral of RT in a greater percentage of patients. Finally, an aggressive management of endocrinological problems, physical and cognitive rehabilitation as well as psychological and school support help provide these children with maximal function within their potential.