The gruesomeness of the action was intensified in the original release by the use of 3-D, with several disembowelments being shot from a perspective such that the internal organs are thrust towards the camera.

Baron von Frankenstein neglects his duties towards his wife/sister Katrin, as he is obsessed with creating a perfect Serbian race to obey his commands, beginning by assembling a perfect male and female from parts of corpses. The doctor's sublimation of his sexual urges by his powerful urge for domination is shown when he utilizes the surgical wounds of his female creation to satisfy his lust. He is dissatisfied with the inadequate reproductive urges of his current male creation, and seeks a head donor with a greater libido; he also repeatedly exhibits an intense interest that the creature's "nasum" (nose) have a correctly Serbian shape.

As it happens, a suitably randy farmhand, Nicholas, leaving a local brothel along with his sexually repressed friend, brought there in an unsuccessful attempt to dissuade him from entering a monastery, are spotted and waylaid by the doctor and his henchman, Otto; mistakenly assuming that the prospective monk is also suitable for stud duty, they take his head for use on the male creature. Not knowing these behind-the-scene details, Nicholas survives and is summoned by Katrin to the castle, where they form an agreement that he will gratify her unsatisfied carnal appetites.

Under the control of the doctor, the male and female creatures are seated for dinner with the castle's residents, but the male creature shows no signs of recognition of his friend as he serves the Baron and his family. Nicholas realizes at this point that something is awry, but himself pretends not to recognize his friend's face until he can investigate further. After a falling-out with Katrin, who is merely concerned with her own needs, Nicholas goes snooping in the laboratory and is captured by the doctor. Frankenstein muses about using his new acquisition to replace the head of his creature, who is still showing no signs of libido. Nevertheless, Katrin is rewarded for betraying Nicholas by being granted use of the creature for erotic purposes, but is killed during a bout of overly vigorous copulation.
Meanwhile, Otto repeats the doctor's sexual exploits with the female creature, resulting in her graphic disembowelment. The Baron returns and, enraged, does away with Otto. When he attempts to have the male creature eliminate Nicholas, however, the remnants of his friend's personality rebel and the doctor is killed in gruesome fashion. The creature, believing he is better off dead, then disembowels himself. The doctor's children, Erik and Monica, then enter the laboratory, pick up a pair of scalpels, and proceed to turn the wheel of the crane that is holding the farmhand in mid-air. It is not clear if the scalpels are there in order to release him, or take over where their father left off.
Joe Dallesandro – Nicholas, the stableboy
Udo Kier – Baron von Frankenstein
Monique van Vooren – Baroness Katrin Frankenstein
Arno Juerging – Otto, the Baron's assistant
Dalila Di Lazzaro – Female Monster
Srdjan Zelenovic – Sacha / Male Monster
Marco Liofredi – Erik, the Baron's son
Nicoletta Elmi – Monica, the Baron's daughter
Liù Bosisio – Olga, the maid
Cristina Gaioni – Farmer, Nicholas' girlfriend
Rosita Torosh – Sonia, the prostitute
Carla Mancini – Farmer
Fiorella Masselli – Large prostitute
Imelde Marani – Blonde prostitute
Miomir Aleksic (uncredited) – Other male monster
Screenwriter Tonino Guerra is better known as the author of Fellini's Amarcord and Antonioni's Blowup.
While some Italian prints reportedly give second unit director Antonio Margheriti credit as director of the film, Udo Kier has stated that Margheriti had nothing to do with directing the film. Kier stated that he and the other cast members received direction only from Morrissey, and noted that he never saw Margheriti on the set.
As a favor for producer Carlo Ponti, Margheriti agreed to take credits for free as director for the Italian release in order to help the film get funds from the government. Unfortunately, it ended up as a trial for producer and alleged director who both lost.
The gory special make-up effects were the work of Carlo Rambaldi, who later went on to create the eponymous alien in Steven Spielberg's "E.T. the Extra-terrestrial" (1984) and the alien that bursts out of actor John Hurt's stomach in Ridley Scott's "Alien" (1979).
The film was later cut to 93 minutes for an R-rating, thereby increasing its viability for wider distribution. It was this version which was distributed for a 3-D re-release during the 3-D craze of the 1980s. The U.S. DVD releases have utilized the full uncut version, which is now unrated. The film had its television premiere in the United Kingdom on November 17, 2009 and was broadcast in 3D as part of Channel 4's 3D Week.
The film earned $4.7 million in rentals in North America.
Upon its release, Nora Sayre of The New York Times wrote "In a muddy way, the movie attempts to instruct us about the universal insensitivity, living-deadness and the inability to be turned on by anything short of the grotesque. However, this 'Frankenstein' drags as much as it camps; despite a few amusing moments, it fails as a spoof, and the result is only a coy binge in degradation."
Craig Butler of AllMovie called the film "a ramshackle affair, with performances that are ludicrously over-the-top and direction that is even more so, and a script that is filled with horrible dialogue. Not to mention, it's a truly gross experience. Of course, many will appreciate it just for these qualities, either to laugh at how truly outrageous it all is or to marvel at the manner in which director/writer Paul Morrissey is skewering the very countercultural sex revolutionaries that were among his biggest fans, creating what is at heart a very conservative critique of hippie culture." Ian Jane of DVD Talk said of the film, "Flesh for Frankenstein is a morbid and grotesque comedy that won't be to everyone's taste but that does deliver some interesting humor and horror in that oddball way that Morrissey has."
Andy Warhol's Frankenstein currently holds a 91% 'fresh' rating on movie review aggregator website Rotten Tomatoes.