Pixelmator 1.3 adds many new tools including click-and-drag Magic Wand, Paint Bucket, and Magic Eraser tools; improved Hue and Saturation, Replace Color, and Colorize tools; and a Smart Palette Hide. The Smart Palette Hide temporarily "dissolves" palettes when any of the adjustment tools or filters are being used.

Performance improvements can be seen across the board when working with images because it takes advantage of Core Image and OpenGL.

Pixelmator 1.3 is a free update for current registered users. For new users the application costs US$59.