The 15 January 1916 Moving Picture World announced that Tyrone Power had joined Universal at its California studio and was working with Phillips Smalley and Lois Weber on The Illborn, the working title of their eugenics film. Two weeks later, the 29 January 1916 Motion Picture News noted that The Illborn was "rapidly nearing a conclusion." The film retained that title through its editing stage and its initial test screening at the Universal City studio theater, according to the 11 March 1916 Moving Picture World.
       Among exterior locations was an area near Hollywood Boulevard and Cosmo Street in Hollywood, CA, which on 29 September 2021 was officially dedicated by the city as Chaplin-Keaton-Lloyd Alley.
       Universal was committed to screening what it called an important motion picture. On 28 March 1916 it arranged a special New York City screening for major religious leaders and three representatives of the National Board of Review, which had already denounced the film on the grounds that its subject matter "might exert a harmful influence on miscellaneous audiences," the 15 April 1916 Moving Picture World reported. The representatives reacted favorably, and suggested only minor changes that wouldn't "seriously alter the tone and meaning of the photoplay."
       A photo-illustrated, full-page Universal advertisement in the 27 May 1916 Motion Picture News ballyhooed the traffic-stopping mob of people outside the Globe Theatre on New York's Broadway, where Where Are My Children? opened on 10 April 1916.
       By June, state rights sales in California alone had paid for the cost of making the film, the 10 June 1916 Motion Picture News reported.
       Where Are My Children? faced censorship challenges all around the country. It was not allowed to be shown in Pennsylvania on the grounds that it tended to debase or corrupt morals. According to a 20 April 1916 Moving Picture World review, the trial of a physician for mailing a book that advocated birth control was "plainly indicative of" the Margaret Sanger case of 1915, in which she was indicted for using the U.S. Postal Service to send pleas for birth control. Universal won a case in Brooklyn, NY, in 1916 to show the film after the district attorney brought suit against the theater manager and the Universal Exchange handling New York's state rights sales.
       The 27 May 1916 Moving Picture World mentioned that Lois Weber cast Mary MacLaren in a small role in Where Are My Children? before giving her the lead in Shoes (1916, see entry).
       The copy of this film that was viewed by AFI Catalog "was reconstructed in 2000 from several incomplete American and European release prints," thanks to "the financial support of the Women's Film Preservation Fund of New York Women in Film and Television." A post-production script guided the order of shots and the language on missing inter-titles. The title is listed in existing prints as Where Are My Children, without the question mark, although it is included in copyright records and contemporary reviews. Some ads in late 1916 showing a backlist of Smalley-Weber titles also omitted the question mark.