organization Media Matters for America named Matthews its 2005 Misinformer of the Year, in part for statements he made in support of President George W. Bush.
On January 9, 2008, the morning after Hillary Clinton's surprise victory in the New Hampshire Democratic presidential primary, Matthews appeared on MSNBC's
Morning Joe program and said of Clinton,
The comments, widely seen as grossly sexist and unfair, were criticized by such disparate media figures as Bill O'Reilly, Joy Behar, and Gloria Steinem. They also resulted in protests outside NBC's Washington, D.C. studios, as well as a joint letter of complaint to NBC from the National Organization for Women, Feminist Majority, and the National Women's Political Caucus. Matthews apologized for the comments on the January 17, 2008 edition of
Hardball.
After controversy following on-air comments that Matthews and Keith Olbermann made during the 2008 Republican National Convention, NBC News correspondent David Gregory replaced them, but Matthews and Olbermann continued as analysts. On November 4—5, he teamed with Rachel Maddow, Eugene Robinson, David Gregory, and Keith Olbermann to cover the presidential election.
During MSNBC's coverage of the Potomac primary, Matthews had this to say about then presidential candidate Barack Obama:
This led many on the right to assert that both he and MSNBC were biased toward Obama.
On November 6, 2008, he was a guest on the MSNBC television program
Morning Joe, where he stated, "I want to do everything I can to make this thing work, this new Presidency work." Host Joe Scarborough asked if that was his job as a journalist. "Yeah, that’s my job. My job is to help this country," Matthews said.
On December 1, 2009, preceding Obama's speech announcing a troop increase in Afghanistan, Matthews critiqued the president for choosing the United States Military Academy as his venue, referring to it as "the enemy camp." Soon after, Matthews apologized for his remarks saying, "[To] the cadets, their parents, former cadets and everyone who cares about this country and those who defend it: I used the wrong words and worse than that I said something that is just not right and for that I deeply apologize."
In January 2010, in Matthews' comments after President Obama's first State of the Union Address, he says "You know, I forgot he was black tonight for an hour." The next day, on the Rachel Maddow show, Matthews clarified his remarks, saying "I think he’s taken us beyond black and white in our politics, wonderfully so, in just a year."