Although he was part of the governing coalition, in December 2005 Baghdasaryan alleged that "serious ballot stuffing" occurred during the November 2005 constitutional referendum.

[2] He stood as Rule of Law's candidate in the February 2008 presidential election and placed third with 17.7% of the vote according to final official results.

[4] Baghdasaryan, unlike some other members of his party, did not take part in the protests against the election led by Ter-Petrossian, however.

[5] On February 29, 2008, he announced that he had accepted the post of Secretary of the National Security Council in a planned coalition government,[4][5] recognizing the legitimacy of the election and the victory of Prime Minister Serzh Sargsyan.

Baghdasaryan currently acts as the chairman of the Board of Trustees of the European University of Armenia.