The beauty of gems and minerals have been examined and appreciated by optical tools for centuries. Current methods for examining the interior structure of gems and minerals typically requires a sample to be cut and polished prior to imaging. In this presentation, we introduce a new tool for imaging gems and minerals in three dimensions, the multiphoton microscope. We have demonstrated that the multiphoton microscope can capture fascinating information from natural gems and minerals with sub-micron resolution at depths up to the millimeter scale. This new application of multiphoton microscopy may open the doors to non-destructive characterization leading to new information on the formation, structure, and appearance of these stones that have fascinated the eye for centuries.