With the introduction of Diagnosis Related Groups (DRG) for reimbursement in 2003 detailed description of the prevalence of pulmonary embolism (PE) in hospitalized patients in Germany was possible for the first time. Thus we estimated the incidence rate of PE in Germany. Detailed lists of all PE coded as I26 performed in 2005, 2006 and 2007 were provided by the Federal Statistical Office. In addition age- and gender-adjusted incidence rates were calculated for all cases for which PEs were coded. In 2005 a total of 67,351, in 2006 a total of 69,234 and in 2007 a total of 71,223 PEs (I26.0) were coded either as principal or secondary diagnosis in German hospitals. 54-57% of all PEs were coded as principal diagnosis. Age- and gender adjusted incidence of PEs raised with increasing ages and were higher in males aged 30-49 and 50-69 years than in females within the same age groups. Up to 60% of all PE documented in females occurred within the 8th and 9th decade of life. Departments of Geriatric Medicine, Haematology and Oncology and Pneumology had the highest rates of intrahospital PEs documented as secondary diagnosis. The presented data are derived from the most reliable data base for the estimation of PE in Germany, and the analysis shows that PE is still a relevant problem. They do not give any information about the individual settings and preventability of PEs. An accompanying analysis of hospital and pre-hospital settings is mandatory to recognize possible strategies to prevent PEs more effectively.