Clumped isotopes geochemistry measures the thermodynamic preference of two heavy, rare, isotopes to bind with each other. This preference is temperature dependent, and is more pronounced at low temperatures. Carbonate clumped isotope values are independent of the carbonate δ13C and δ18O, making them independent of the carbon or oxygen composition of the solution from which the carbonate precipitated. At equilibrium, it is therefore a direct proxy for the temperature in which the carbonate mineral formed. In most cases, carbonate clumped isotopes record the temperature of carbonate formation, irrespective of the mineral form (calcite, aragonite, or bioapatite) or the organism making it. The carbonate formation temperatures obtained from carbonate clumped isotope analysis can be used in conjunction with the δ18O of the same carbonate, to constrain the oxygen isotope composition of the water from which the carbonate has precipitated. There are, however, cases of deviation from thermodynamic equilibrium, where both clumped and oxygen isotopes are offset from the expected values. Such carbonates must be characterized and calibrated separately. For deep-time applications, special care must be paid to the preservation of the original signal, in particular with respect to diagenetic alteration associated with atomic scale diffusion that may be undetectable by common tests for diagenesis.