Cancer therapy includes surgery, chemotherapy and irradiation. Depending on the diagnosis, the location of the neoplasm and the age of the patient, these treatment modalities may be given alone or in combination. All forms of cancer therapy can affect the hypothalamic-pituitary-gonadal axis. The long-term consequences for reproductive function depend on several aspects. The sex of the patient is important, since ovarian and testicular function differ significantly. Sex hormone production in the female is dependent on the presence of germ cells, whereas this is not the case in the male. The sensitivity of germ cells to cancer therapy also differs between the sexes. Moreover, the sensitivity of both the hypothalamic-pituitary axis and the gonads is highly age dependent. With regard to chemotherapy, the possible damage to the gonads is dependent on the total dose and type of agent given. According to current knowledge, the hypothalamic-pituitary axis is not affected by conventional doses of chemotherapy. Radiotherapy has by far the most damaging effect on the reproductive axis, having serious adverse effects on both the hypothalamic-pituitary area as well as on the gonads themselves. The harmful effect of irradiation depends on the total dose of irradiation, the radiation field, as well as the number and size of fractions given. The long-term consequences of recently introduced radiotherapeutic methods such as stereotactic irradiation are not yet known. The present review will focus on the late effects of cancer therapy in children and young adults with acute lymphoblastic leukaemia, non-Hodgkin’s lymphoma, brain tumour, Hodgkin’s lymphoma or Wilms’ tumour, including the adverse effects of bone marrow transplantation.