An estimated 49 percent of LGBT people live in states with laws banning marriage, and 37 percent live in states with constitutional bans on any form of relationship recognition.
Same-sex marriage is legal in six states and the District of Columbia. Maryland and Washington state are poised to enact laws doing the same.
But while these families get the same benefits as heterosexual families in states where marriage is legal, they do not at the federal level.
"The most stressful piece is financial," said Laura Deaton, policy research director for the Movement Advancement Project and lead researcher on the report.
For low-income families, that means less money to meet basic needs, and for others, it may make it more difficult to save for a child's education.
"Our tax system has always been very pro-family and designed to create an incentive that encourages people to live in families and to support their children," said Deaton. "But that is not there for same-sex couples."
"It's kind of ironic," she said. "These are families who do the same work, but the same rules don't apply."
Bourdon and his husband both work at universities, but they say it is difficult to find CPAs who have expertise in their unique tax situation. Those who are knowledgeable in the field can charge from $500 to $4,000 for such a return.
"It's so much more complicated and you pay a lot more money to get professional help," said Bourdon, so he does it himself with the online program Turbo Tax, which is attuned to the needs of same-sex parents.
"I just hope I am doing it right," he said. "They steer you in the right direction."
One spouse will take the house as a deduction on the federal return.
"Jimmy and I make a fairly close salary," said Bourdon. "Still, what I end up doing is having to run so many different scenarios -- which one will help or harm us financially."
"It's absolutely absurd," said MAP Executive Director Ineke Mushovic. "Essentially, the federal government is asking families to lie."
Legal groups have begun to advise LGBT parents who are married to indicate on their tax forms that the only reason they are checking the box as "single" or "head of household" is because they are required to do so, according to Mushovic.
Some in California file the required "single" returns then file an amended return so "it's on the record," say advocacy groups.
Congress held a hearing on DOMA repeal last summer and now several LGBT couples and their families are making legal challenges that are working their way through the courts.
Bourdon sees the same financial inequities when the children of LGBT parents apply for financial aid at the college level.
Not only are they forced to lie on the form -- if they have two moms or two dads, they can only list one of them and their financial details," he said. "It could benefit you or hurt you."
But some employers are now leveling the playing field for their LGBT employees who are married by "grossing up" their incomes, according to Bourdon. "It doesn't give you any more money, but you end up in the same place. They try to erase the inequity."
But the law still makes LGBT families feel "clearly stigmatized and not accepted," he said.
"When people feel like they have to hide for so long about their identity and family -- and no we don't have to anymore -- but we are forced to lie again [by the government.]"
Still, Bourdon is optimistic that the laws will eventually catch up with the changing cultural mores.
"Absolutely, I feel that the tide is turning and people are starting to see more acceptance for same-sex partnerships," he said. "But we are still burdened by so many unfair laws that deny us protection in employment and housing and relationship status.
"And we live in a country where the federal government doesn't recognize our relationships."