The job is an expanded version of the old science & research post, and comes just months before the first European Innovation Act is due to be published.
The creation of an innovation commissioner has been well flagged, with European Commission President José Manuel Barroso having repeatedly pledged to streamline innovation policy (EurActiv 24/09/09).
Ann Mettler, executive director of the Lisbon Council, a Brussels-based think-tank, said the new role did not come as a surprise and would be "a cross-cutting" portfolio that works across several departments.
"It's important that the new commissioner embodies innovation within the Commission and challenges the conventional wisdom," she said.
One element of the new portfolio which remains unclear is precisely how the move affects the Commission's DG Enterprise – now called 'Industry & Entrepreneurship' – which is currently charged with drafting the Innovation Act.
Mettler said it would be wrong to view the reshuffle as a battle between commissioners, as she expects to see greater "sharing of ownership" in Barroso's new team.
"The old silo approach is the antithesis of innovation," she said. Mettler added that it will be interesting to see who launches the new Innovation Act, and suggested it could be a joint initiative between the commissioners for innovation and industry.
The Commission has also revealed that the new European Institute for Innovation & Technology (EIT) will be run by the education commissioner. This too is an initiative likely to be of interest to Geoghegan Quinn.
The EIT is seen as a pet project of President Barroso and has recently moved into its new headquarters in Budapest. The first of its flagship 'Knowledge and Innovation Communities' (KICs) will be announced on 16 December.
The education portfolio has been handed to outgoing Health Commissioner Androulla Vassiliou, who will now be responsible for the Marie Curie Programme unit, which previously rested with DG Research.