Stressor-response research on stony corals in the laboratory relies on detecting relatively small changes in the size of coral fragments throughout the course of an experiment. Coral colonies are complex, three-dimensional (3D) communities of organisms, so small changes in size are best detected by changes in 3D surface area. Traditional methods to estimate 3D coral surface area commonly require destruction of the sample, thereby eliminating repeat measurements and the ability to calculate growth rate. However, non-destructive two-dimensional (2D) photogrammetry can be used if defensible relationships with 3D surface area can be established. In this study, 165 coral skeletons representing four stony coral species (Pocillopora damicornis, Madracis mirabilis, Orbicella faveolata, Porites porites) were photographed in 2D (top and side views) and then imaged with 3D laser scanning. Significant linear relationships were found between the 3D surface areas (laser) and the sum of various combinations of top and side view surface areas captured by 2D digital photography. The relationships were very strong for simple colony shapes and more variable as coral fragments increased in size and complexity. This study demonstrates an efficient method for obtaining estimates of 3D coral surface area from non-destructive 2D photogrammetry, allowing measurement of growth rate throughout experimental exposure periods.