"Wherever we stand politically, whatever commitments and ideas we may have, we are bound by the united will and respect for the identity of our peoples, and ever closer union of our peoples as provided in the treaties," he said.
The other candidates in the election were Jens-Peter Bonde, a Dane who heads the Independence/Democracy group and Francis Wurtz, a French communist politician.
Poettering's election in the year's first plenary session in Strasbourg was never in any doubt as he received firm backing from the Socialists, the second biggest group in the parliament.
The two main rival parties struck a compromise in 2004 in the wake of elections to share the presidency of the parliament, with its two seats in Brussels and Strasbourg.
Under that deal, a socialist was to be president for the first half of the parliament's five-year term and a conservative would then take over until 2009.
Parliament has gained more influence as co-legislator with the council of EU governments on a range of policies, from internal market rules to the environment.
Poettering stood down last week after seven years as chairman of the centre-right European People's party, the parliament's largest group and which includes the governing parties of France and Germany.