Diving deep into the controversial movement from the early 20th century, aimed at improving society by encouraging the reproduction of certain traits, Thomas also charged that Planned Parenthood founder Margaret Sanger was once "particularly open about the fact that birth control could be used" for eugenic purposes.
Why eugenics? At the core, Thomas was explaining his thinking about an Indiana abortion law that bans abortion motivated solely by the race, sex or disability of the fetus. But critics say he was also taking up an oft-used argument made by opponents of abortion who say the procedure threatens those deemed undesirable by society.
"We denounce eugenics in all forms for the same reason we are working to fight abortion bans across the country," said Melanie Newman, senior vice president of communications and culture for Planned Parenthood Federation of America. "Every person should have the freedom to make their own decisions about their body."
The opinion came on Tuesday, when the court said it would leave in place a lower court opinion that invalidated a provision in Indiana's law.
In an unsigned opinion, the court reasoned that only one federal appeals court has addressed such a law, and that it would "follow our ordinary practice" and stay away from the issue until other courts have had a chance to weigh in.
Thomas concurred in the opinion that allowing "further percolation" was acceptable, but he stressed that the court's action should not be interpreted as an "agreement" with the lower court.
In making his point, Thomas dedicated more than a dozen pages on the history of the eugenics movement to explain why "the use of abortion to achieve eugenic goals is not merely hypothetical."
Wading through history, he noted that some eugenicists believed that the "distinction between the fit and the unfit could be drawn along racial lines," and others would define a person as "feeble-minded."
In 1927, the Supreme Court, Thomas pointed out, "threw its prestige behind the eugenics movement" in its decision upholding the constitutionality of Virginia's forced-sterilization law in Buck v. Bell.
He said that while the court's decision gave the eugenics movement "added legitimacy," support for eugenics waned considerably by the 1940s as "Americans became familiar with the eugenics of the Nazis and scientific literature undermined the assumptions on which the movement was built."
Thomas said he was prompted to address the history of the movement because the case at issue "highlights the fact that abortion is an act rife with the potential for 'eugenic manipulation'" and he urged his colleagues that they could "not avoid" such issues forever.
"Having created the constitutional right to an abortion, this Court is dutybound to address its scope," Thomas said.
Jessica Levinson, a professor of law at Loyola Law school notes that Thomas in his opinion suggests that the fetus is being discriminated against.
"He may try to place abortion laws under the rubric of anti-discrimination laws" in the future, Levinson said.
Critics say that what Thomas was doing in the opinion is adopting a tactic of the anti-abortion movement.
"For a long time, opponents of abortion have charged that abortion threatens those deemed undesirable in society," said Johanna Schoen, a professor of history at Rutgers University.
"In arguing that Indiana's law that bans abortion based solely on race, disability or sex, could one day pass legal muster, Thomas is harkening back to the eugenics movement of the early 20th century," she said.
But Schoen, who supports abortion rights and has written a book called "Abortion after Roe," argues the comparison is invalid.
"Eugenics -- at its core -- is based on the state making reproductive decisions for others. Indiana's law basically does the same thing, limiting a woman's reproductive autonomy," she said.
"He is tying eugenics to particular reproductive technologies -- here abortion -- instead of recognizing that eugenic laws robbed women of their ability to make their own reproductive decisions -- the state decided for them," Schoen said.
Schoen acknowledges that Sanger did adopt some of the eugenics framework in order to gain the support of medical professionals in the 1920s and '30s. But Sanger was arguing for access to birth control.
"She was advocating for women's rights, not for selective breeding," Schoen said.
Indeed, Thomas did allow that Sanger distinguished between birth control and abortion. But he said, "The arguments that she made in support of birth control apply with even greater force to abortion."