To document baseline levels of coral disease we use two 25 m belt transects with visual counts at each site. A team of two divers swim along the transects, with one diver identifying and enumerating coral colonies within a 25m x 2m (100 m2 reef area) belt transect, while the other diver records occurrence of disease within a wider 25m x 6m transect (250m2 reef area). Corals are identified to the species level and assigned to one of seven size classes (0-5cm, 6-10cm, 11-20cm, 21-40cm, 41-80cm, 81-160cm and > 160cm). This methodology yields quantitative estimates of coral size distributions, recruitment, density, diversity and prevalence of disease. Diseased corals are photographed and a general description of the condition is recorded. Samples of diseased coral (and healthy portions for controls) are collected for laboratory investigations using microbiological, molecular and histopathological techniques. Coral cover is estimated using either line-intercept method or digital photography.