At the trial, the prosecution sought to have entered into evidence a fingerprint card with Clay Shaw's signature on it and, which also had on it, Shaw's admission that he had used the alias "Clay Bertrand." In regard to this, Judge Edward Haggerty, after dismissing the jury, conducted a day long hearing, in which he ruled the fingerprint card inadmissible. He said that two policemen had violated Shaw's constitutional rights by not permitting the defendant to have his lawyer present during the fingerprinting. Judge Haggerty also announced that Officer Habighorst had violated Miranda v. Arizona and Escobedo v. Illinois by not informing Clay Shaw that he had the right to remain silent. The judge said that Habighorst had violated Shaw's rights by allegedly questioning him about an alias, adding, "Even if he did [ask the question about an alias] it is not admissible." Judge Haggerty exclaimed, "If Officer Habighorst is telling the truth — and I seriously doubt it!" The judge finished with the statement, "I do not believe Officer Habighorst!"
Jim Garrison's key witness against Clay Shaw was Perry Russo. Russo testified that he had attended a party at the apartment of anti-Castro activist David Ferrie. At the party, Russo said that Lee Harvey Oswald (who Russo said was introduced to him as "Leon Oswald"), David Ferrie, and "Clem Bertrand" (who Russo identified in the courtroom as Clay Shaw) had discussed killing Kennedy. The conversation included plans for the "triangulation of crossfire" and alibis for the participants.Russo’s version of events has been questioned by some historians and researchers, such as Patricia Lambert, once it became known that some of his testimony was induced by hypnotism and by the drug sodium pentothal, sometimes called "truth serum." 
In addition to the issue of Russo's credibility, Garrison's case also included other questionable witnesses, such as Vernon Bundy, a heroin addict, and Charles Spiesel, who testified that he had been repeatedly hypnotized by government agencies. However, defenders of Garrison, such as journalist and researcher Jim Marrs, argue that Garrison's case was hampered by missing witnesses that Garrison had sought out. These witnesses included right-wing Cuban exile, Sergio Arcacha Smith, head of the CIA-backed, anti-Castro Cuban Democratic Revolutionary Front in New Orleans, a group that David Ferrie was reputedly "extremely active in", and a group that maintained an office in the same building as Guy Bannister. According to Garrison, these witnesses had fled New Orleans to states whose governors refused to honor Garrison's extradition requests. However, Sergio Arcacha Smith had left New Orleans well before Garrison began his investigation  and was willing to speak with Garrison's investigators if he was allowed to have legal representation present Further, witnesses Gordon Novel from Ohio may have been extradited if Garrison pressed the case in Ohio and Sandra Moffett was offered by the defense but opposed by Garrison's prosecution.
At the trial's conclusion — after the prosecution and the defense had presented their cases — the jury took 54 minutes on March 1, 1969, to find Clay Shaw not guilty.More mind control?
In a 1992 interview, Edward Haggerty, who was the judge at the Clay Shaw trial, stated: "I believe he [Shaw] was lying to the jury. Of course, the jury probably believed him. But I think Shaw put a good con job on the jury."
In On the Trail of the Assassins, Garrison states that Shaw had an "...extensive international role as an employee of the CIA." Shaw denied that he had had any connection with the CIA.
In 1979, Richard Helms, former director of the CIA, testified under oath that Clay Shaw had been a part-time contact of the Domestic Contact Service of the CIA, where Shaw volunteered information from his travels abroad, mostly to Latin America.
In 1996, the CIA revealed that Clay Shaw had obtained a "five Agency" clearance in 1949.
A quick search of the FOIA database at cia.gov gives these references, of course none of available for download:
CLAY L. SHAW'S TRIAL AND THE CENTRAL INTELLIGENCE AGENCY
Doc No/ESDN: CIA-RDP79-00632A000100100004-5
AMERICAN, 'NOWHERE ELSE TO GO; COMES HERE TO TELL FANTASTIC TALE LINKS CIA WITH OSWALD, CLAY SHAW
Doc No/ESDN: CIA-RDP75-00149R000600020007-0
CLAY SHAW OF THE CIA
Doc No/ESDN: CIA-RDP75-00149R000700210017-7
Some links to G.H.W. Bush: