Filming commenced October 13, 1938 on the MGM Studios lot in Culver City, California, under the direction of Richard Thorpe (replacing original director Norman Taurog, who only filmed a few early Technicolor tests and was then reassigned). Thorpe initially shot about two weeks of footage (nine days, total) involving Dorothy's first encounter with the Scarecrow, as well as a number of sequences in the Wicked Witch's castle, such as Dorothy's rescue (which, though unreleased, comprises the only footage of Buddy Ebsen's Tin Man).
Ten days into the shoot, however, Ebsen suffered a reaction to the aluminum powder makeup he wore; the powder he breathed in daily as it was applied had coated his lungs. Ebsen was hospitalized in critical condition, and subsequently was forced to leave the project; in a later interview (included on the 2005 DVD release of The Wizard of Oz), Ebsen recalled the studio heads initially disbelieving that he was seriously ill, only realizing the extent of the actor's condition when they showed up in the hospital as he was convalescing in an iron lung. Ebsen's sudden medical departure caused the film to shut down while a new actor was found to fill the part. No full footage of Ebsen as the Tin Man has ever been released — only photographs taken during filming and test photos of different makeup styles remain. MGM did not publicize the reasons for Ebsen's departure until decades later, in a promotional documentary about the film. His replacement, Jack Haley, simply assumed he had been fired. Ironically, despite his near-death experience, Ebsen outlived all of the principal cast members by at least sixteen years, although his film career was damaged by the incident.
Producer Mervyn LeRoy had taken this time to review the already shot footage and felt that Thorpe seemed to be rushing the picture along, creating a negative impact on the actors' performances; thus, LeRoy decided to have Thorpe replaced. During reorganization on the production, George Cukor temporarily took over, under LeRoy's guidance. Initially, the studio had made Garland wear a blond wig and heavy, "baby-doll" makeup, and she played Dorothy in an exaggerated fashion; now, Cukor changed Judy Garland's and Margaret Hamilton's makeup and costumes, and told Garland to "be herself." This meant that all the scenes Garland and Hamilton had already completed had to be discarded and re-filmed. Cukor also suggested that the studio cast Jack Haley, on loan from 20th Century Fox, as the Tin Man. To keep down on production costs, Haley only rerecorded "If I Only Had a Heart" and solo lines during "The Jitterbug" and "If I Only Had the Nerve"; as such, Buddy Ebsen's voice can still be heard in the remaining songs featuring the Tin Man in group vocals. The makeup used for Haley was quietly changed to an aluminum paste, with a layer of clown white greasepaint underneath to protect his skin; although it did not have the same dire effect on Haley, he did at one point suffer from an unpleasant eye infection from it.
In addition, Ray Bolger's original recording of "If I Only Had a Brain" had been far more sedate compared to the version heard in the film; during this time, Cukor and LeRoy decided that a more energetic rendition would better suit Dorothy's initial meeting with the Scarecrow (initially, it was to contrast with his lively manner in Thorpe's footage), and was re-recorded as such. At first thought to be lost for over seven decades, a recording of this original version was rediscovered in 2009.
Cukor did not actually shoot any scenes for the film, merely acting as something of a "creative advisor" to the troubled production, and, because of his prior commitment to direct Gone with the Wind, he left on November 3, 1938, at which time Victor Fleming assumed the directorial responsibility. As director, Fleming chose not to shift the film from Cukor's creative realignment, as producer LeRoy had already pronounced his satisfaction with the new course the film was taking.
Production on the bulk of the Technicolor sequences was a long and cumbersome process that ran for over six months, from October 1938 to March 1939. Most of the actors worked six days a week and had to arrive at the studio as early as four or five in the morning, to be fitted with makeup and costumes and would not leave until seven or eight at night. Cumbersome makeup and costumes were compounded by the fact that the early Technicolor process required a significant amount of lighting to be used (due to the low ASA speed of the film), which would usually heat the set to over a hundred degrees. According to Ray Bolger, most of the Oz principals were banned from eating in the studio's commissary due to their costumes. Margaret Hamilton's witch makeup meant that she could not eat solid food, so she practically lived on a liquid diet during filming of the Oz sequences. Additionally, it took upwards of 12 takes to have Dorothy's dog Toto run alongside the actors as they skipped down the Yellow Brick Road.
All of the Oz sequences were filmed in three-strip Technicolor. The opening and closing credits, as well as the Kansas sequences, were filmed in black and white and colored in a sepia tone process. Sepia-toned film was also used in the scene where Aunt Em appears in the Wicked Witch's crystal ball.
The massive shoot also proved to be somewhat chaotic. This was most evident when trying to put together the Munchkinland sequences. MGM talent scouts searched the country far and wide to come up with over a hundred little people who would make up the citizens of Munchkinland; this meant that most of the film's Oz sequences would have to already be shot before work on the Munchkinland sequence could begin. According to Munchkin actor Jerry Maren, each little person was paid over $125 a week for their performances. Munchkin Meinhardt Raabe, who played the coroner, revealed in the 1990 documentary The Making of the Wizard of Oz that the MGM costume and wardrobe department, under the direction of designer Adrian, had to design over one hundred costumes for the Munchkin sequences. They then had to photograph and catalog each Munchkin in his or her costume so that they could correctly apply the same costume and makeup each day of production.
Filming even proved to be dangerous, at times. Margaret Hamilton was severely burned in the Munchkinland scene, and as she tells the story on the DVD commentary: "There was a little elevator that was supposed to take me down, with a bit of fire and smoke erupting to dramatize and conceal my exit. The first take ran like clockwork, I went down out of my clothes, the fire and smoke erupted and that's the one you see." But for the second take, the timing was off, and she was exposed to the flames. The grease in her copper-based makeup caught fire and had to be completely and quickly removed before the ensuing second-degree burns on her hands and face could be treated. After spending some six weeks in the hospital convalescing, she returned to the picture.
On February 12, 1939, Victor Fleming hastily replaced George Cukor in directing Gone with the Wind; the next day, King Vidor was assigned as director by the studio to finish the filming of The Wizard of Oz (mainly the sepia Kansas sequences, including Judy Garland's singing of "Over the Rainbow"). In later years, when the film became firmly established as a classic, Vidor chose not to take public credit for his contribution until after the death of his friend Fleming in 1949.
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