"Begotten" was first conceived as an experimental theater piece with dance and live musical accompaniment, but Merhige switched to film after deciding that his vision would be too expensive to achieve as a production for live audiences. Antonin Artaud and philosopher Friedrich Nietzsche were major influences on "Begotten", as Merhige believed their ideas and theories had not been explored in film to their full extent. The film's visual style was inspired by Georges Franju's documentary short "Blood of the Beasts", Akira Kurosawa's "Seven Samurai", Stan Brakhage's "The Act of Seeing with One's Own Eyes", and the German Expressionist film "The Cabinet of Dr. Caligari". "Begotten" was shot on location in New York and New Jersey over a period generally thought to have been three and a half years although, in an interview, Merhige said filming took only five and a half months.