Van Gogh's "Flowers in a Blue Vase" was found by researchers to be damaged by chemicals.
The chemicals in the varnish, applied after the work was complete, was found to turn the artist's beloved yellows gray.
Researchers at the University Antwerp, examining the work with X-rays, found during conservation efforts that the cadmium yellow had lost its richness and had become gray, said BBC News.
Scientists were confused by the color changes, which were not just a fading of the protective coating.
"Varnish can become brown with age and thus can give all colors a more dark tone," study author Koen Janssens, of the University of Antwerp, told LiveScience.
Cadmium yellow often fades but does not necessarily turn grayish.
The researchers found that the paint, not just the varnish, had turned a flat color.
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The study saw samples of the painting handed over to Europe's largest X-rays for examination to determine what was going on at the atomic level.
The X-rays of Van Gogh's painting found that negatively charged sulfate ions had linked with lead ions from the varnish.
From there, they worked to form anglesite, a lead-sulfate compound which tends to be gray in color, said LiveScience.
The investigators suggested two solutions to the problem: keep the painting in low-light conditions and start using a more modern varnish.
Van Gogh's "Flowers in a blue vase" was painted in 1887 in Paris.
It was then acquired by the Kröller-Müller Museum in the Netherlands in the early 20th century.