Apatite is the most abundant crystalline phosphate mineral found as an accessory mineral in practically all kinds of igneous rocks. Sometimes it is concentrated in pegmatites, metallic veins and magmatic deposits. It also occurs in metamorphic rocks and as a secondary mineral in phosphatic rocks of sedimentary origin. Rock phosphates (or phosphorites) are sedimentary phosphatic deposits comprising fine grained mixture of various calcium phosphates, most important being hydroxyl-apatite, carbonate-apatite, flour-apatite and their solid solutions. About 80% phosphate production in the world is derived from phosphate rocks (phosphorite) containing one or more phosphatic minerals, usually calcium phosphate of sufficient purity and quantity to permit its use directly or after concentration in manufacturing commercial products.

Apatite is a group of phosphate minerals, usually referring to hydroxylapatite, fluorapatite, and chlorapatite, named for high concentrations of OH-, F-, or Cl- ions, respectively, in the crystal. The formula of the admixture of the three most common endmembers is written as Ca5(PO4)3(OH, F, Cl), and the formulae of the individual minerals are written as Ca5(PO4)3(OH), Ca5(PO4)3F and Ca5(PO4)3Cl, respectively.

Fluorapatite (or fluoroapatite) is more resistant to acid attack than is hydroxyapatite. For this reason, toothpaste typically contain a source of fluoride anions (e.g. sodium fluoride, sodium monofluorophosphate). Similarly, fluoridated water allows exchange in the teeth of fluoride ions for hydroxyl groups in apatite. Too much fluoride results in dental fluorosis and/or skeletal fluorosis.

Fission tracks in apatite are commonly used to determine the thermal history of orogenic (mountain) belts and of sediments in sedimentary basins. (U-Th)/He dating of apatite is also well-established for use in determining thermal histories and other, less typical applications such as paleo-wildfire dating.

Phosphorite is a phosphate-rich sedimentary rock, that contains between 18% and 40% P2O5. The apatite in phosphorite is present as cryptocrystalline masses referred to as collophane.

Apatite is occasionally found to contain significant amounts of rare earth elements and can be used as an ore for those metals. This is preferable to traditional rare earth ores, as Apatite is non-radioactive and does not pose an environmental hazard in mine tailings.