About 60 million years ago, tectonic movements of the Earth's crust began to uplift the Colorado Plateau, of which the Painted Desert is part. Eventually parts of the plateau rose to 10,000 feet above sea level. This warping of the Earth's surface led to the gradual and continuing destruction of the plateau by erosion.

An unconformity (break in the rock record) of about 200 million years occurs within the park, where erosion has removed all the rock layers above the Chinle except geologically recent ones. The Bidahochi Formation, laid down only 4 to 8 million years ago, rests directly atop the Chinle, and rocks laid down in the Jurassic, Cretaceous, and much of the Tertiary are absent.