Coral reefs are constructed by calcifiers that precipitate calcium carbonate to build their shells or skeletons through the process of calcification. Accurately assessing coral calcification rates is crucial to determine the health of these ecosystems and their response to major environmental changes such as ocean warming and acidification. Several approaches have been used to assess rates of coral calcification but there is a real need to compare these approaches in order to ascertain that high quality and intercomparable results can be produced. Here, we assessed four methods (total alkalinity anomaly, calcium anomaly, 45Ca incorporation and 13C incorporation) to determine coral calcification of the reef-building coral Stylophora pistillata. Given the importance of environmental conditions on this process, the study was performed under two pH (ambient and low level) and two light (light and dark) conditions. Under all conditions, calcification rates estimated using the alkalinity and calcium anomaly techniques as well as 45Ca incorporation were highly correlated. Such a strong correlation between the alkalinity anomaly and 45Ca incorporation techniques has not been observed in previous studies and most probably results from improvements described in the present paper. The only method which provided calcification rates significantly different from the other three techniques was 13C incorporation. Calcification rates based on this method were consistently higher than those measured using the other techniques. Although reasons for these discrepancies remain unclear, the use of this technique for assessing calcification rates in corals is not recommended without further investigations.