Filming
Principal photography took place from February 14, 1990, to May 8, 1990, over a course of 83 days on an $18.3 million budget. The house exterior scenes were filmed on location at a three-story single-family house located at 671 Lincoln Avenue in the North Shore village of Winnetka, Illinois, where many of Hughes's previous films had also been shot, but at different houses. The only interiors of the house used for filming that made it to the finished film were the main staircase, attic and most of the first floor landing, while all the other interiors of the house were duplicated on a sound stage to allow more room for equipment and crew. These sets were built in the then-disused gym of New Trier High School's west campus, previously used by Hughes for Uncle Buck and Ferris Bueller's Day Off, where the production company had already set up its offices. 671 Lincoln Avenue later became a tourist attraction. The tree house in the backyard was built specifically for the film and dismantled after filming ended.
Kevin runs away from his third encounter with Marley in Hubbard Woods Park in Winnetka. In addition, the scene where Kevin wades in his neighbor's flooded basement was shot at the empty swimming pool of the aforementioned campus of New Trier High School, with the American Airlines DC-10 first class cabin interiors done on the basketball courts. The church exteriors were shot at Trinity United Methodist Church in Wilmette, Illinois, while the interiors were shot at Grace Episcopal Church in Oak Park, Illinois. Filming also took place over four sixteen-hour days at O'Hare International Airport, which served for both itself and Orly Airport in Paris. John Candy filmed his cameo appearance for the film over the course of one day at Meigs Field.
For the film within a film, Angels with Filthy Souls (the title of which parodies the 1938 crime film Angels with Dirty Faces), shooting took one day, on the final "test day" prior to the official start of principal photography. To create the illusion that the film was an authentic 1940s gangster film, the scene was filmed on black-and-white negative film, and Johnny's office featured props from that era. Like much of the film, most of the sequence was shot with low, wide angles that, according to journalist Darryn King, "capture the action as if a child were perceiving it". Originally, Ralph Foody was to play Snakes and Michael Guido was to play Johnny, but since Foody had recently undergone knee replacement surgery, he was unable to do the death scene where Snakes drops to his knees, leading to the roles being switched.
Cinematographer Julio Macat recalled that Pesci was more difficult to work with than Culkin. The older actor believed some of the dialogue was not of a quality commensurate with his acting ability. He also resented the early unit calls, since they prevented him from starting his day with nine holes of golf as he preferred to do. After he took the assistant director by the collar one day to complain about this, daily call times were moved back from 7 to 9 a.m. to accommodate his rounds. However, strict child labor laws limiting Culkin to a 10 p.m. finish meant the crew had limited time to shoot night scenes.
During the scene where Kate forces her son, Kevin, to sleep in the attic due to him misbehaving, O'Hara struggled to say the line "Then say it again, it'll maybe happen" as she found it horrific to say to a child.
Pesci said in a 2022 interview with People of working with Culkin, "I intentionally limited my interactions with him to preserve the dynamic" and made sure not "to come across on the screen that we were in any way friendly" in order to "maintain the integrity of the adversarial relationship".
On the set, Pesci and Stern both had difficulty refraining from cursing, which became annoying to Pesci, since Culkin was on set as well. The curse words that made it into the film were "shit", accidentally said by Daniel Stern when his shoe fell through the pet door, and "hell", which was said by both Pesci and Stern after their characters encounter one another after going through Kevin's booby traps and by Johnny to the character of Snakes in Angels with Filthy Souls. Pesci's use of "cartoon cursing", or menacing gibberish, garnered comparisons to Looney Tunes character Yosemite Sam.
The film's stunts also created tension for the crew during shooting. Columbus said, "Every time the stunt guys did one of those stunts it wasn't funny. We'd watch it, and I would just pray that the guys were alive." Stunts were originally prepared with safety harnesses, but because of their visibility on camera, the film's final stunts were performed without them. Troy Brown and Leon Delaney were stuntmen for Pesci and Stern, respectively. An injury had occurred between Pesci and Culkin during one of the rehearsals for the scene in which Harry tries to bite off Kevin's finger; Culkin still has the scar. The tarantula that walks on Stern's face was real.
Senta Moses, who played Tracy, recalled in 2020 that one of the most difficult scenes to shoot was the family's run through O'Hare International Airport to catch their flight. While it does not last long, it required several days to film. "There were thousands of extras, all expertly choreographed so none of us would be in danger running at full speed through the American Airlines terminal", she told The Hollywood Reporter. "And we ran at full speed. Sometimes we'd bump into each other, like a multi-car pileup on the expressway, and just crack up laughing ... There were so many setups and narrowly missed moments of disaster, but to my knowledge, no one got hurt."