BACKGROUND: Malignant germ cell tumors (GCTs) are a rare and a heterogeneous group of pediatric cancers. The incidence rate has increased in some populations or subgroups. However, only a few recent publications on epidemiologic data showing the trends in incidence of pediatric GCTs are available. METHODS: We analyzed the incidence rates, time trends, and survival for 1366 GCTs in children 0 to 14 years old registered in the nationwide, population-based German Childhood Cancer Registry in 1987–2011. RESULTS: The incidence rate of GCTs was slightly higher in girls (age-standardized rate: girls, 5.3; boys, 4.4 per million). A bimodal age distribution was seen. In children aged <1 year, the highest age-specific incidence rates were seen for girls with GCTs in the pelvis (12.7 per million) and for boys with GCTs in the testis (9.5 per million). For 10- to 14-year-old boys, the tumors occurred most often in the central nervous system (3.1 per million); for girls, the most common site was in the ovaries (4.5 per million). Only the incidence rate for ovarian GCTs increased statistically significantly. The 5- and 20-year survival probabilities for the patients diagnosed between 1987 and 2010 were 92% and 90%, respectively. Survival rates improved notably for intracranial and extragonadal GCTs from 1987 to 2006. CONCLUSIONS: The localization and histology of the GCTs varied between the genders and age groups. During 1987 to 2011, the incidence rate increased only for ovarian GCTs. The increase, however, may be due to changes in reporting. The survival rates were excellent.