Many of Hannah's scenes were filmed in Mia Farrow's own apartment. Woody Allen said that Farrow once had the eerie experience of turning on the television, finding a chance broadcast of the movie, and seeing her own apartment on television--while she was sitting in it.
While parts of the film were being shot in her apartment, Mia Farrow and several of her children lived and went about their daily routines on a working film set and among the crew. The Farrow family ws careful not to interrupt production, or to do anything that would affect the shooting schedule; however, the situation was hectic for family and crew alike. Co-star Michael Caine likened the situation to watching an intimate home movie, and recalled that one moment Farrow would be feeding her children dinner and the next the assistant director would inform her that she was needed on set. She would put down the kitchen utensils, walk into the next room and begin to act.
Woody Allen says he was inspired by the title. "I thought I'd like to make a film called 'Hannah and Her Sisters'," he said, saying this prompted him to give Hannah two sisters. He was interested in making something about the relationship between sisters, which he felt was more complex than that between brothers. "Maybe that comes from childhood; my mother had seven sisters, and their children were female, so all I knew were aunts and female cousins."
Part of the film's structure and background is borrowed from Ingmar Bergman's Fanny and Alexander (1982). In both films a large theatrical family gathers for three successive years' celebrations (Thanksgiving in this film, Christmas in Bergman's). The first of each gathering is in a time of contentment, the second in a time of trouble and the third showing what happens after the resolution of the troubles. The sudden appearance of Mickey's reflection behind Holly's in the closing scene also parallels the apparition behind Alexander of the Bishop's ghost. Additional parallels can be found with Rocco and His Brothers (1960), which, besides the connection to its name, also uses the structural device of dividing sections of the film for the different siblings' story arcs.
Woody Allen admits that the role of Hannah was based on Mia Farrow being "a romanticized perception of Mia. She's very stable, she has eight children now, and she's able to run her career, and have good relationships with her sister and her mother. I'm very impressed with those qualities, and I thought if she had two unstable sisters, it would be interesting."
Michael Caine plays Mia Farrow's husband. In real life, Caine had been a long-term friend to both Farrow and Woody Allen, then a couple. In fact, Caine had been the one who introduced the couple to each other nearly 20 years before.
Mia Farrow wrote that "it was the first time I criticized one of his scripts. To me, the characters seemed self-indulgent and dissolute in predictable ways. The script was wordy, but it said nothing." She claims that "Woody didn't disagree, and tried to switch over to an alternative idea, but pre-production was already in progress, and we had to proceed." She elaborated, "It was my mother's stunned, chilled reaction to the script that enabled me to see how he had taken many of the personal circumstances and themes of our lives and, it seemed, had distorted them into cartoonish characterizations. At the same time he was my partner. I loved him. I could trust him with my life, and he was a writer, this is what writers do. All grist for the mill. Relatives have always grumbled. He had taken the ordinary stuff of our lives and lifted it into art. We were honored and outraged".
This film marked the first collaboration between Woody Allen and cinematographer Carlo Di Palma, and launched a decade-long partnership. Allen had worked with Gordon Willis in all of his films since 1977; however Willis was not available due to a scheduling conflict.
Mia Farrow later wrote that Woody Allen had been intrigued about the subject of sisters for a long time. Janet Margolin, one of his earlier co-stars, had two sisters, Diane Keaton had two and Farrow had three. She says Allen gave her an early copy of "Hannah and Her Sisters", saying she could play whatever sister she wanted, but that "he felt I should be Hannah, the more complex and enigmatic of the sisters . . . whose stillness and internal strength he likened to the quality Al Pacino projected in The Godfather (1972)."
Frederick, played by Max von Sydow, complains bitterly, while watching television, that if Jesus were to come back and see what religion had become, "he'd never stop throwing up." Von Sydow played Jesus in The Greatest Story Ever Told (1965).
According to the script, Elliot and Lee (Michael Caine and Barbara Hershey) were supposed to act out a heated love scene in a boat. The scene was to be remarkably lengthy and explicit, something that had been absent from Woody Allen's previous films. Due to the lack of precedent, Caine and Hershey figured that the scene would be cut from the script before it was ever filmed. Much to their chagrin, it was not. The scene was filmed, and while it called for no nudity, the actors were required to provide realistic movements to simulate sex in a lengthy scene. Much to the actors' relief, the whole sequence was cut from the final film.
Mia Farrow admitted "a small sick feeling . . . deep inside me" which "I shared with nobody was my fear that 'Hannah and Her Sisters' had openly and clearly spelled out his feelings for my sister. But this was fiction, I told myself . . . so I put those thoughts out of my mind."
The structure of the film, centering around holiday gatherings, was based on Fanny and Alexander (1982) by Ingmar Bergman. Woody Allen had long been an admirer of Bergman's films. This may also explain the inclusion of Max von Sydow, a Bergman regular, in the cast. In fact, Von Sydow had wanted to be in Fanny and Alexander, but demands, made on his behalf by his agent, prevented his involvement.
Woody Allen and John Turturro would later appear in Fading Gigolo (2013) in reversed roles. Allen directed, wrote and acted alongside Turturro in a supporting role in Hannah and Her Sisters (1986), while in the other film Turturro was the lead actor, writer and director, with Allen playing a supporting role.