Most minerals are composed of two or more elements with their atoms arranged in a regular structure, called a crystal lattice or crystal structure. In chemistry, this is known as a compound. To visualize crystal structure, think of balls attached to other balls with sticks to make regular three-dimensional patterns. The balls represent atoms and the sticks represent the forces between the atoms. Electromagnetic forces between atoms hold some chemical compounds together. In other compounds, the atoms form covalent bonds, which means they share electrons. Scientists classify many minerals into groups based on the types of atoms found in the minerals. For example, oxides consist of metallic atoms bound to oxygen atoms, and sulfides are combinations of metal and sulfur atoms.

One of the most striking, yet least diagnostic, features of many minerals is their color. Well-formed mineral crystals span the entire rainbow of tinctures, from red (cinnabar, garnet) to yellow (sulfur), green (malachite), blue (azurite, lazurite), and violet (the amethyst variety of quartz). Minerals containing iron and magnesium are often dark brown or dark green. Impurities, trace amounts of elements that do not normally belong in the mineral, may change the overall color of a crystal. For instance, depending on the trace amounts of impurities it contains, quartz may look colorless (no impurities), light pink (titanium, iron, or manganese), milky white (tiny bubbles of gas or liquid), purple (iron), yellow (iron), or brown (extra silicon). However, multiple minerals may have almost the same color, so scientists must rely on other physical properties to make definite identifications of mineral specimens.

Gemstones are minerals that are cut and polished to make beautiful "stones" for jewelry and other adornments. Humans traditionally consider diamonds, rubies, sapphires, and emeralds to be the four "precious" gemstones, with all other gemstones called "semiprecious." Many gems are transparent, meaning they allow some or most of the incident light to pass through them. To make a stone sparkle, gemcutters cut and polish the facets, or flat outer surfaces, of a gemstone to boost the number of times a light beam will reflect internally before leaving the stone and reaching the eye. Some semiprecious stones, such as malachite and lapis lazuli (a rock containing the mineral lazurite), are opaque to light; gemcutters polish them to a high gloss, without facets. This shiny, rounded type of gemstone is called a cabochon. Corundum (ruby or sapphire) specimens that contain tiny fibers of other minerals also may be cut into cabochons to create a luminous "star" effect on the stone's surface.