The defense had challenged the evidence since it was obtained using new DNA technology that had not been tested in a New York court.
Prosecutors successfully argued the technology was derived from accepted scientific methods.
Judge Timothy Mazzei ruled that nuclear DNA results obtained from rootless hairs recovered from Maureen Brainard-Barnes, Megan Waterman, Amber Costello, Sandra Costilla, Jessica Taylor and Valerie Mack are admissible at trial.
Mazzei said the use of whole genome sequencing to extract DNA from the hairs, create a profile and then compare that profile to Heuermann "is generally accepted in the relevant scientific community."
The judge said he based the decision on expert testimony, peer-reviewed articles and use of the technology in other states, including California and Idaho.
"We won, the evidence is admissible," Suffolk District Attorney Ray Tierney said. "Full speed ahead for trial."
Experts say nuclear DNA, which has been used clinically but not in a case like this, could have broader implications for other cold cases.
"Because this technology allows us to do what we couldn't do before with old samples, degraded samples that are just too small. There's just too little DNA. This opens up the doors to use samples that we didn't even think we could," said Professor Nathan Lents of John Jay College of Criminal Justice.
But it also opens doors for the defense.
"Hopefully enlighten the jury wherethey'll neutralize this type of testimony or they won't give it any credit, and we're back to mitochondrial DNA," said defense attorney Michael Brown.
The defense answered by filing a motion claiming Astrea Forensics' work is in violation of the state Public Health Law, because the lab is not accredited in New York state.
Prosecutors say the DNA links hairs from six of the seven victims to Rex Heuermann, his wife and daughter.
"Obviously that's a key factor in this case," Tierney said.
Relatives of Heurmann's alleged victims stood behind prosecutors but did not speak publicly. Heuermann's wife was also at court but said nothing.
What is clear is Heuermann's defense will continue to question the new DNA evidence before a jury.
"We'll attack it during the course of the trial and we'll attack it effectively," Brown said.
The defense is also still waiting for a decision on its motion to break up the case into multiple trials. Mazzei said he would rule on that later this month at the next hearing scheduled September 23 .
Tierney reiterated a plea deal is not on the table.
The decision marks the first time such techniques are allowed as evidence in a New York court - and one of just a handful of such instances nationwide.
"Obviously this is another tool in our toolbox," Tierney said, agreeing that it could allow more cold cases to move forward for prosecution.
(ABC News contributed to this report.)
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