He's the "absolute worst" pick, according to The Nation magazine's Sarah Posner, who said that his selection is a "slap in the face".
"Warren vocally opposes gay marriage, does not believe in evolution, has compared abortion to the Holocaust and backed the assassination of Iranian President Mahmoud Ahmadinejad," she writes.
Divider, not a uniter
Joe Solmonese, president of the Human Rights Campaign, said Obama's selection represents a "genuine blow" to the gay community.
"By inviting Rick Warren to your inauguration, you have tarnished the view that gay, lesbian, bisexual and transgender Americans have a place at your table," Solmonese writes.
"In this case, we feel a deep level of disrespect when one of architects and promoters of an anti-gay agenda is given the prominence and the pulpit of your historic nomination," he adds.
Let me count the ways
People For the American Way President Kathryn Kolbert says Warren hardly deserves "this position of honor".
"It is a grave disappointment to learn that pastor Rick Warren will give the invocation at the inauguration of Barack Obama," she said in a statement before outlining her main concerns with the selection.
"He has recently compared marriage by loving and committed same-sex couples to incest and pedophilia," she begins. "He has repeated the Religious Right's big lie that supporters of equality for gay Americans are out to silence pastors. He has called Christians who advance a social gospel Marxists. He is adamantly opposed to women having a legal right to choose an abortion."