We report on a nested case–control study with 328 cases with second malignant neoplasm (SMN) following childhood cancer and 639 matched controls based on the German Childhood Cancer Registry. In the adjusted overall analysis, the odds ratio (OR) for SMN following any radiotherapy or chemotherapy is 2.1 [95% confidence interval (CI): 1.8–3.31 and 1.8 (95% CI: 0.98–3.1), respectively. The strongest effect is seen for alkylating agents (OR= 2.0, 95% CI: 1.2–3.3). The risk of SMN after leukemia is pronounced for antimetabolites (OR= 17.2, 95% CI: 1.7–177) and asparaginase (OR= 4.3, 95% CI: 1.7–11.0). Following solid tumors, the greatest effect is seen for platinum derivatives (OR= 4.1, 95% CI: 1.7–10.1). For anthracyclines, a decreased risk is observed (OR= 0.3, 95% CI: 0.1–0.6). Secondary solid tumors are mainly associated with radiotherapy (OR= 4.5, 95% CI: 2.5–8.0), especially secondary carcinomas. Secondary acute myeloid leukemia and myelodysplastic syndrome are mainly associated with alkylating agents (OR= 8.5, 95% CI: 0.97–74.8), asparaginase (OR= 6.8, 95% CI: 2.3–20.6), and platinum derivatives (OR= 4.5, 95% CI: 1.5–13.6). The observed risks are in many instances lower than the ones published in previous studies relating to earlier treatment eras of the primary diseases. These differences may be attributed to less toxic but still effective treatment regimes but also to differences in the length of follow-up.