Connected to internal radiation damage, these processes partially disrupt the crystal structure and partly explain the highly variable properties of zircon. As zircon becomes more and more modified by internal radiation damage, the density decreases, the crystal structure is compromised, and the color changes.

Zircon occurs in many colors, including reddish brown, yellow, green, blue, gray, and colorless. The color of zircons can sometimes be changed by heat treatment. Common brown zircons can be transformed into colorless and blue zircons