The protests came as a new effort gets underway to get the state to define marriage as only between a man and woman.
The new civil union law goes into effect on June 1st. A person will be able to enter into a civil union with same-sex or different-sex partners.
June 2nd is the day that same-sex Illinois couples can enter into civil unions that will provide them with the same state rights as married couples.
The Americans for Life group protested the Illinois law on civil unions and kicked off a statewide petition drive to legally define marriage as being between one man and one woman. The rally started at St. Peter's Catholic Church in the Loop.
"The civil unions bill has been shoved down our throat without the people having a chance to vote on it," said Richard Walsh of Americans for Life.
"I am outraged that these people over here would desecrate a church run by Franciscans with their bigotry and their hatred this is not about holding up the sanctity of marriage," said Rick Garcia. "It is against gay people pure and simple."
"We are not shouting hate, we are praying for them," said Tommie Romano. "And that's what we do: we pray for them."
Gay activists staged a counter protest across from the church demanding their rights to a civil union.
"Civil unions are really important to my partner and me because we have a child, and this will be one extra way of solidifying our family," said Ann Jordan Baker.
"We are actually very good parents - my daughter of 22 years has two dads," said Mike Lakovich.
A civil union is not a marriage. Illinois law continues to exclude gay and lesbian couples from marriage.
Civil unions provide gay and lesbian couples legal benefits and protections.
Both groups left the church and marched to the Thompson Center to voice their concerns.
"We're announcing an advisory referendum petition to put on the ballot in 2012 to call on the legislature to pass a binding marriage amendment which would protect marriage - the definition between one man and one woman," said Peter LaBarbera of Americans for Truth.
You must be at least 18 years old to take part in a civil union.
The Illinois civil union law does not apply to other states. That means you cannot transport your civil union.
A civil union must be dissolved in court like divorce rather than simply by notifying your local county clerk.
Hundreds are expected to show up at the clerk's office on June 1st for civil union licenses.
They must wait until the next day to have a ceremony officiated by a judge or a religious order.