Despite the fact that most of the shorts from this series were later shown on its spin-off House of Mouse - Il Topoclub (2001), there were shorts from Mickey Mouse Works (1999) that were never shown in the spin-off, which were "Minnie Takes Care of Pluto" and the "Pluto Gets the Paper" short, "Vending Machine". These two shorts were only aired once on ABC, and were later banned from reruns on The Disney Channel and Toon Disney for their dark and violent nature, and were never included in any episodes of House of Mouse - Il Topoclub (2001). However, the shorts can still be seen on international airings.
Several of the Donald Duck cartoons from this show were released on DVD in 2008 as part of "Walt Disney Treasures: The Chronological Donald, Volume 4" (1951-1961).
This was the first time Daisy Duck was voiced by Tress MacNeille alongside Diane Michelle part-time.
This show premiered the same day as the premiere of Nickelodeon's SpongeBob SquarePants on May 1, 1999.
The first Mickey Mouse television series to be completely animated.