William McMurry, the plaintiffs' solicitor, said on Thursday that the ruling could open the way to take depositions of Vatican officials and to obtain copies of church records and documents.
"Our whole purpose is to hold the Vatican accountable," McMurry said.
Many lawsuits stemming from the clergy sex abuse crisis have named the pope, the Vatican and other high-ranking church officials as defendants. But the Holy See is typically immune from the jurisdiction of US courts.
Only last month, the Los Angeles Roman Catholic Archdiocese, the largest in the US, said it would pay $60 million to settle 45 of the more than 500 claims against it claiming sexual abuse by its priests, in a move to stem the spiralling sex abuse crisis.
Orders of conduct
In a BBC documentary produced last year, a reporter traced the sexual abuse crisis back to the Vatican and to Pope Benedict XVI himself.
According to the report, while Pope Benedict was still Cardinal Raztinger, he authorised a document in 2001, which was then approved by the late Pope John Paul related to crimes of solicitation. The document instructed all bishops to put the interests of the church ahead of those of law enforcement.
Apparently, the document was an updated version of the notorious 1962 Vatican document Crimen Sollicitationis - Latin for The Crime of Solicitation - which laid down the Vatican's strict instructions on covering up sexual scandal. It was regarded as so secret that it came with instructions that bishops had to keep it locked in a safe at all times.
The Vatican published guidelines on how to deal with paedophile priests on January 8, 2002, saying all cases should be reported to Rome.
Last October, Benedict addressed the crisis by saying that the wounds from sexual abuse in the Church "run deep", and instructed bishops to do whatever necessary to prevent repeat offences and rebuild confidence.
Benedict has taken a much clearer line on sexual abuse than his predecessor the late John Paul. Last May, he disciplined the elderly Mexican founder of a Roman Catholic religious group who had been accused of sexual abuse, ordering him to retire to a life of "prayer and penitence".
John G. Heyburn II, US district judge, dismissed claims that the Holy See was negligent by failing to protect children entrusted to the clergy. He also threw out claims of deceit and misrepresentation by the Vatican.
Jeffrey Lena, a California-based attorney for the Vatican, said the ruling was in many respects favorable to the Holy See because the remaining allegations rely on the unproved assumption that US bishops act as agents of the Vatican. He predicted that claim would not be borne out as the case proceeds.
Vatican officials declined to comment.
McMurry is seeking to have the lawsuit certified as a class action, which would allow other accusers to join the case. McMurry represented 243 victims of sexual abuse that settled with the archdiocese in 2003 for $25.3 million.
One of the three plaintiffs is Michael Turner of Louisville, who also filed the first lawsuit against the archdiocese.
The Reverend Louis E. Miller was removed from the priesthood in 2004 by the late Pope John Paul II after pleading guilty in 2003 to sexually abusing Turner and other children in the 1970s. He is serving a 13-year prison sentence.
The two other plaintiffs, James H. O'Bryan and Donald E. Poppe, have not settled. Both live in California and allege that they were abused by priests while growing up in Louisville.