The application, which has been featured on every Windows release since 1985, was listed as "Deprecated" in the company’s Windows 10 Fall Creators Update.
While Microsoft did not say specifically that MS Paint would be removed, the company defined features and functionalities that are "Deprecated" as those that "are not in active development and might be removed in future releases."
Outcry from users and coverage by news organizations about the loss of the classic image-editing application prompted Microsoft to set the record straight.
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"MS Paint is not going away. In addition to the new 3D capabilities, many of the MS Paint features people know and love like photo editing and 2D creation are in Paint 3D - the new app for creativity, available for free with the Windows 10 Creators Update," a Microsoft spokesperson said.
"In the future, we will offer MS Paint in the Windows Store also for free and continue to provide new updates and experiences to Paint 3D so people have the best creative tools all in one place."
On Monday, a blog post shared by Windows Experiences acknowledged the "incredible outpouring of support and nostalgia" around the application.
"MS Paint is here to stay."