The Supreme Court debated Tuesday whether Maryland’s decision to collect DNA samples from people arrested for serious crimes represents an unconstitutional invasion of privacy or a crime-solving breakthrough with the potential to be the “fingerprinting of the 21st century.”

Either way, Justice Samuel A. Alito Jr. said, the case is “perhaps the most important criminal procedure case that this court has heard in decades.”

At issue are laws in 29 states and on the federal level that allow some version of DNA collections. And the oral argument highlighted the difficulty the court sometimes has in squaring emerging or potential technological advances with centuries-old constitutional protections.

“How can I base a decision today on what you tell me is going to happen in two years?” Chief Justice John G. Roberts Jr. asked Maryland Chief Deputy Attorney General Katherine Winfree. “Don’t I have to base a decision on what we have today?”

As with many criminal procedure cases, it brought together justices who often are on opposite sides of the court’s ideological divide. Justices Antonin Scalia and Elena Kagan, for instance, were the most critical of Maryland’s law; Alito and Justice Stephen G. Breyer seemed most supportive.

In this photo taken Oct. 8, 2010, the U.S. Supreme Court justices pose for a group photo at the Supreme Court in Washington. (Pablo Martinez Monsivais/AP)

For instance, when Winfree opened her argument by saying that Maryland’s law since 2009 had resulted in “225 matches, 75 prosecutions and 42 convictions,” Scalia pounced.

“That proves absolutely nothing,” the justice said. “I’ll bet you if you conducted a lot of unreasonable searches and seizures, you’d get more convictions, too.”

And Breyer was one of the toughest questioners faced by the attorney for Alonzo Jay King Jr., whose DNA was taken after a 2009 arrest for assault and later used to connect him to an unsolved rape.

“I can argue that it is certainly a much lesser intrusion than fingerprints,” Breyer said of the inner-cheek swabs used to collect DNA samples. And “it’s much more accurate, and that doesn’t just help the defendant,” Breyer said. The innocent are protected when a DNA match identifies the true perpetrator, he said.

Maryland, backed at the court by all the states, the District of Columbia and the Obama administration, allows the collection of DNA samples from those arrested for, but not yet convicted of, a crime of violence, an attempted crime of violence, a burglary or an attempted burglary. If the arrest does not lead to a conviction, the sample is supposed to be destroyed.

King was convicted of rape after the DNA match. But the Maryland Court of Appeals overturned the conviction and the state’s law, saying it violated the Constitution’s protection against unreasonable searches and seizures. Roberts has kept the ruling from going into effect until the Supreme Court could consider the issue, and Maryland has continued the DNA collections.

Winfree said DNA is the most accurate way for identifying a person in custody, allowing courts to make informed decisions about bail and discovering whether the person is tied to other crimes.

“This is the fingerprinting of the 21st century, but it’s better,” Winfree said. “Typically, DNA evidence is used to identify rapes and murderers. Fingerprints typically do not solve those kinds of crimes.”

But Winfree immediately ran into trouble. While Maryland’s law is limited, the state’s argument is expansive, some justices said.

“Under your theory, there’s no reason you couldn’t undertake this procedure with respect to anybody pulled over for a traffic violation,” Roberts said.

Justices Ruth Bader Ginsburg and Elena Kagan questioned whether the collection of DNA from an arrestee who is not suspected of any other crimes could be compared to a search that is not based on reasonable suspicion.

“It could be any arrestee, no matter how minor the offense,” Kagan said. “It could be just any old person in the street. Why don’t we do this for everybody who comes in for a driver’s license, because it’s very effective?”

But Deputy Solicitor General Michael R. Dreeben, representing the federal government, said arrestees “are on the gateway into the criminal justice system. They are no longer like free citizens who are wandering around on the streets retaining full-impact Fourth Amendment rights.”

“Yes, but that doesn’t mean, for example, that you can go into their house without a warrant,” Roberts said.

Dreeben said that was because such a search would reveal things that have an expectation of privacy under the law and a person’s DNA does not.

It was a proposition Roberts later used when King’s attorney, Kannon K. Shanmugam, came to the podium. Shanmugam said his client’s rights were compromised when he was searched “without a warrant in order to investigate crimes for which there was no suspicion.”

But Roberts wondered what the privacy expectation could be when DNA can be collected from a drinking glass or a cigarette butt or “when it’s left wherever you happened to have been.”

Shanmugam was repeatedly pressed on why the DNA collections were different from fingerprints. He said DNA could tell much more about a person’s life, and that fingerprints are used mostly to identify a person, while DNA is being used to try to connect an arrestee to other crimes.

That did not bother Alito. “So this is what is at stake,” Alito said. “Lots of murders, lots of rapes that can be solved using this new technology that involves a very minimal intrusion on personal privacy.”

But Shanmugam said there could be a great intrusion. “I don’t think there can be any dispute that when you evaluate the entirety of an individual’s DNA, there is a great deal of personal information contained there,” he said.

“The government’s response to that is essentially the ‘just trust us’ defense,” he said.

The case is Maryland v. King .