The German Childhood Cancer Registry regularly presents graphs of childhood cancer incidence rates by period, but no systematic analysis. The Automated Childhood Cancer Information System-project found an increasing trend in Europe. Against this background we present the first detailed trend analysis of childhood (aged under 15) malignancies in Germany. We examined incidence rates separately in western Germany 1987-2004 and eastern Germany 1991-2004. We analyzed all malignancies, all main diagnostic groups and relevant subsets using an age-period-cohort model. Additionally we fitted fractional polynomials to assess the linearity of the drift. All malignancies combined (excluding Central Nervous System-tumors and neuroblastoma) show a significant trend: +0.7% in western and +1.1% per year in eastern Germany. The overall trend in Germany is mostly due to the significant increase in lymphoid leukemia, which increased significantly in western Germany (+0.7% per year) and significantly nonlinearly in eastern Germany (+3.3% per year until 1998, +0.8% since 1998), catching up from a level 20% below western Germany. This could be due to life style changes since the reunification in eastern Germany influencing early immune system training. We found no trends for acute non-lymphocytic leukemia and non-Hodgkin lymphoma. Hodgkin's disease shows a cohort effect in western Germany after reunification. Improved registration of CNS tumors led to an increase. Neuroblastoma yielded a period effect in western Germany due to screening. With the exception of germ cell tumors, further observations for solid tumor entities are in agreement with those reported for Europe.