Inside a mineral, atoms arrange themselves into a specific, repeating pattern called a crystal lattice or crystal structure. The smallest three-dimensional arrangement within the lattice is called a "unit cell," which is duplicated over and over again symmetrically. At the level of the everyday world, minerals that are growing without outside interference tend to form crystals that resemble their underlying crystal structures. Scientists call that kind of general, typical appearance a "crystal habit." Of course, conditions that existed during a mineral's formation or crystal growth may change its habit, but geologists still find this attribute to be a useful tool for identifying minerals. Scientists use more than three dozen adjectives to describe crystal habits. For example, natrolite and rutile can be acicular, or needlelike; quartz often forms hexagonal prisms; pyrite and halite typically crystallize as cubes; and mica is foliated or lamellar (layered).

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.