With the introduction of diagnosis-related groups (DRG) for reimbursement in 2003, detailed description of the prevalence of pulmonary embolism in hospitalized patients in Germany was possible for the first time. Thus, we analysed the incidence of pulmonary embolism in hospitalized young people and looked for a sex-specific difference in comorbidity. Detailed lists of all pulmonary embolism coded as I26 in hospitalized patients aged 10-40 years in 2005, 2006 and 2007 were provided by the Federal Statistical Office. Beginning at the age of 12-13 years females have higher numbers of pulmonary embolism and DVT documented as principal diagnosis compared with men. This sex-specific difference disappears at the ages of 32-33 years. The total numbers of pulmonary embolism distinguishing males and females within this 20 years life period is low and varied from 318-463 in the 3 years. The sex-specific difference is highest in the group of 16 to 17-year-old people (ratio of females to males varies from 3 to 5 in 2005-2007). Specific patterns of comorbidities associated with the higher numbers of pulmonary embolism in younger females could not be detected. Pregnancies account for a maximum of 73 in 2007, which reached only less than one-fifth of the absolute difference in pulmonary embolism between males and females in the single years. The presented data derived from the most reliable data basis for the estimation of pulmonary embolism in Germany show that compared with males there is a sharp increase in hospitalization for pulmonary embolism in females beginning at the age of 12-13 years. Males catch up by the ages of 32-33 year.