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The film opens with the following written acknowledgment: "Twentieth Century-Fox acknowledges with thanks the generous cooperation of the United States Marine Corps in the production of Heaven Knows, Mr. Allison." At the end of the film, the comma in Heaven Knows, Mr. Allison is replaced by a period to read Heaven Knows. Mr. Allison. Although the nun is called "Sister Angela" in the film, the Variety review lists her as "Sister Angelica."
Hollywood Reporter news items yield the following information about the production: In July 1952, Eugene Frenke purchased the rights to Charles Shaw's novel. Under the terms of their contract, Shaw was to receive ten percent of the profits. Shaw's generous financial arrangement caused financing difficulties, forcing Frenke to relinquish his ownership of the rights, according to a November 1953 news item in Publishers Weekly. In December 1953, Los Angeles Examiner reported that John Wayne and Robert Fellows had attempted to buy the rights to the novel, but Frenke regained control. Wayne had intended to star, but was replaced by Kirk Douglas after losing the rights. In May 1954, a Hollywood Reporter news item stated that Paramount was negotiating with Frenke for the rights and William Wyler was slated to direct.
An April 1954 Hollywood Reporter news item noted that in the film's original plot, the female lead had stolen a nun's habit and was posing as a sister to elude the Japanese. The Catholic Church rejected this story line because the woman and the Marine fall in love. In the Shaw novel, however, the female protagonist was a nun. In May 1954, Wyler submitted a new story line that was approved by the Church. A modern source adds that the project was shelved after Wyler lost interest. A late April 1954 news item noted that Frenke was negotiating with several studios to produce the film. A May 1954 Daily Variety item noted that Charles Feldman purchased the rights from Frenke and would co-produce the picture with him. By June 1954, Hollywood Reporter announced that Twentieth Century-Fox had bought the rights to the novel as a vehicle for Clark Gable. In December 1955, John Lee Mahin was borrowed from Louis B. Mayer to write the screenplay and, according to a June 4, 1956 Hollywood Reporter news item, Anthony Mann was to direct the film and Ellis St. Joseph was to write the script.
According to a November 1956 New York Times news item, the picture, which began production under John Huston's direction in August 1956, was shot on location in the West Indies to qualify it as a British quota picture. Modern sources note that the Marines featured in the cast were based in Trinidad and add Fusamoto Takasimi, Noboru Yoshida and Anna Sten to the cast; however, Sten was not in the released film. Deborah Kerr was nominated for an Academy Award for Best Actress, but lost to Ingrid Bergman in Anastasia.