This is something that was debated among geologists for years. It is only in the last 15-20 years that we have really begun to understand the causes. The presence of finely-spaced structures in the mineral. What we see as color is the result of our brain's interpretation of the dominant wavelength of light. Minerals are colored because certain wavelengths of incident light are absorbed, and the color we perceive is produced by the remaining wavelengths that were not absorbed.
Some minerals are colorless.
This means that none of the incident light has been absorbed. Color and Atomic Structure Electrons in atoms are located in orbitals around the nucleus. The number of orbitals present is related to the atom's position on the periodic table. The energy of each orbital is precisely defined and is different than that of the adjacent orbitals. Orbitals closer to the nucleus are lower energy than the outer orbitals.