A judge in the Southern District of New York ruled Tuesday that Flagstar Bancorp will have to pay Assured Guaranty Municipal Corp. more than $90 million for defective mortgages packaged in residential mortgage-backed securities (RMBS).

U.S. District Judge Jed Rakoff ruled that Flagstar must pay $90.1 million to Assured for misrepresenting loans in insured securities. Flagstar must also pay interest, attorneys’ fees, and other costs to be determined.

In his ruling, Rakoff said the case “essentially reduces to a resolution of conflicting expert testimony.” In the end, he sided with Assured’s underwriting expert, who testified that more than 75 percent of the loans collected in a random sample of 800 loans showed evidence of “material breach” of Flagstar’s representations and warranties.

In a statement released Tuesday, Assured president and CEO Dominic Frederico called the decision “an important victory” that “sets a strong precedent in support of the rights of Assured Guaranty in these cases.”

“The court recognized and clearly articulated the responsibility of an R&W [representations and warranties] provider to honor its contractual obligations to purchase defective mortgage loans,” Frederico said. “His decision establishes clear liability as it relates to originators and securitizers of RMBS transactions and strengthens Assured Guaranty’s resolve to seek full recovery from R&W providers that refuse to recognize this liability.”

Assured has also pursued Credit Suisse and UBS over similar allegations.

The ruling may indeed set a precedent for other insurers to take advantage of. MBIA Insurance Corporation has filed its own suit against Flagstar for allegedly breaching loan warranties and has another suit against Bank of America over mortgages originated by Countrywide.

What lasting effect Tuesday’s ruling will have is still unclear, however, as it may be turned around. Flagstar issued a statement following the decision, saying that the company “strongly disagrees with the Court’s ruling and intends to vigorously contest the outcome on appeal.”