Dr Soumya Swaminathan was one of the three deputy director-generals supporting the director-general in overseeing all programmes. She was the first Indian to hold the position at WHO.
Dr Swaminathan will now be chief scientist in a newly created department in the WHO.
The revamp, laid out in an internal memo sent to staff and seen by Devex, includes the creation of new positions and divisions which will help WHO achieve its triple billion targets in its new five-year strategic plan.
Zsuzsanna Jakab, currently regional director at WHO in Europe, will be the new deputy director-general.
A globally recognised researcher on tuberculosis and HIV, Dr Swaminathan has been on several committees of WHO and global advisory bodies, including the WHO Expert Panel to Review Global Strategy and Plan of Action on Public Health, Innovation and Intellectual Property, the Strategic and Technical Advisory Group of the Global TB Department at WHO and as co-chair of the Lancet Commission on TB.