The department takes over the role from the defunct Department for Education and Skills, which adopted the Teenage Pregnancy Unit from the Department of Health in 2003. The former Education Secretary, Alan Johnson, moved to become Health Secretary last week.
Charities called for ministers to co-ordinate departments so health strategies for young people remain on target.
Simon Blake, chief executive of Brook, said: "The key thing is to work together to ensure clear leadership and that young people remain a priority for Johnson."
Helen Roberts, professor of child health at the Institute of Education, said: "Johnson should look at issues young people feel are important, such as transport and climate change."
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