CHICAGO, Aug. 28th The American Medical Association led an effort to destroy the chiropractic profession by depriving its practitioners of association with medical doctors and by calling them ''unscientific cultists'' or worse, a Federal district judge has ruled.

Judge Susan Getzendanner described the conspiracy as ''systematic, long-term wrongdoing and the long-term intent to destroy a licensed profession'' in a ruling late Thursday in an antitrust lawsuit filed in 1976.

The decision said the nation's largest physicians' group led a boycott by doctors intended ''to contain and eliminate the chiropractic profession.''

Dr. Alan Nelson, chairman of the A.M.A. board of trustees, said in a telephone interview today from Salt Lake City, ''we don't think there was ever a boycott or a conspiracy.''

Chiropractic is a method of treatment based on the theory that disease is caused by interference with nerve function, which practioners try to correct by manipulating the spine and other joints.

In addition to ''labeling all chiropractors unscientific cultists and depriving chiropractors of association with medical physicians, injury to reputation was assured by the A.M.A.'s name-calling practice,'' Judge Getzendanner said.

The lawsuit, filed by four chiropractors, accused the Chicago-based A.M.A., four of its officials and 10 other medical groups of conspiring to prevent chiropractors from practicing in the United States. Remedy to Be Worked Out

Judge Getzendanner held that the American College of Surgeons and the American College of Radiology had participated in the conspiracy with the medical association. Thomas Greeson, attorney for the Reston, Va.-based radiologists' group, said he was studying the ruling and would have no immediate comment. The spokeswoman for the Chicago-based surgeons' group, Linn Meyer, was not at work and unavailable for comment, an aide said.

The judge set a Sept. 4 meeting of the parties to determine a remedy.

The lawsuit sought no monetary damages, but it challenged the defendants' refusal to acknowledge chiropractors' professional abilities.

''To me, the decision is wrong because we have had a policy which has been very clear for a long time that it is not unethical to associate with a chiropractor if you believe that it is in the patient's best interest,'' said Kirk Johnson, the A.M.A.'s general counsel. Appeal Called Likely

The plaintiffs were to submit ''some kind of proposed injunction'' by Sept. 4, Mr. Johnson said, adding that a decision on an appeal would be made when the injunction was issued.

''I am absolutely convinced the A.M.A. will appeal,'' said the plaintiffs' attorney, George McAndrews. ''The four chiropractors have weathered 11 years of hell to call the A.M.A. and its co-conspirators into account.''

Michael Pedigo of San Leandro, Calif., a plaintiff, said he and other chiropractors wanted ''to be allowed to compete freely in the marketplace.''

He said A.M.A. policy had forbidden doctors from referring patients to chiropractors or accepting referrals from them, though some doctors ignored those rules. The boycott also extended to medical education, with doctors forbidden to lecture before chiropractic classes, he said.

Other plaintiffs were Dr. Chester Wilk of Park Forest, Ill, Dr. Patricia Arthur of Dayton, Ohio, and Dr. James Bryden of Sedalia, Mo.

Judge Getzendanner said the function of the A.M.A.'s Committee on Quackery formed in 1962 was to destroy the chiropractic profession.

The panel was presented with evidence that ''some physicians believed chiropractic to be effective and that chiropractors were better trained to deal with muscular-skeletal problems than medical physicians,'' she said.

The medical association contends the anti-chiropractic effort ended in 1980. Judge Getzendanner said that the organization ''had never acknowledged the lawlessness of its past conduct and maintains to this day it has always been in compliance with antitrust laws.''

''There has never been an affirmative statement by the A.M.A. that it is ethical to associate with chiropractors,'' she said. Other Charges Dismissed

The judge dismissed charges against the American College of Physicians, the Joint Commission on Accreditation of Hospitals and the American Academy of Orthopedic Surgeons. Charges were also dismissed against James H. Sammons of Chicago, an A.M.A. trustee who had served as head of the Committee on Quackery, which was disbanded in 1974. Charges against three other officials of the medical association had been dismissed earlier.

Five defendants settled earlier, affirming the rights of chiropractors. They were the Illinois Medical Society, the American Hospital Association, the Chicago Medical Society, the American Osteopathic Association and the American Academy of Physical Medicine and Rehabilitation.