Theron McGriff of Idaho Falls appealed to the high court after a magistrate ruled in 2002 that he could no longer see his two daughters if he lived with his partner of many years.
"We feel it would be especially inappropriate for the court to get involved in the gender of Theron's partner," said Richard Hearn, representing McGriff. "There is no evidence that this had any impact on the children."
In 1938, Hearn said, the Idaho Supreme Court found that a mother could not be denied custody because she remarried three weeks after her divorce, though at the time such behavior was stigmatized. The court made a similar ruling when presented with a parent suffering seizures from epilepsy, Hearn said.
A county magistrate had sided with McGriff's ex-wife, Shawn Weingartner, in the case. She said she feared the children would suffer backlash in conservative Idaho Falls because of their father's sexuality. She wanted McGriff to undergo counseling about how to present his relationship to the girls.
Marie Tyler, representing Weingartner, told the high court that McGriff refused to speak to his ex-wife about the matter as the animosity between them grew.
"This is about a parent who refuses to cooperate and puts his needs ahead of his children," she said.
Some justices questioned the motives behind the custody dispute.
"The only thing I can find here are several allegations with regard to an intimate relationship with the same sex," said Justice Wayne Kidwell.
Chief Justice Linda Copple Trout noted that the children - now ages 13 and 9 - are fully aware that their father is gay.
Tyler and Weingartner have declined to talk to reporters.
Hearn and McGriff said outside the courthouse that they're optimistic the court will rule in McGriff's favor. A ruling is expected by the end of the year.
"My children were so young when I started dating my partner, they don't remember a time without him. They've told me that we've always been a family," McGriff said.
His partner is living with family members instead of in the home the two bought together, McGriff said.
By Rebecca Boone