<p>Numerous low-lying, unconsolidated carbonate reef islands occur on the shallow reefs of the South China, Sulu and Celebes Seas off the coast of Sabah, at the northeastern end of Borneo. A range of sources, including maps and charts, as well as freely available satellite imagery, has been used to map the location of these islands, identify them, and develop a classification. A total of 44 reef islands were differentiated into: a) sandy areas visible on top of shallow reef flats, b) islands of low elevation, and c) islands of small area (many less than 1 ha). These reef islands were classified based on a) the presence of vegetation and density of vegetation cover, and b) the degree and identification of infrastructure development and human disturbance on the islands. Of the 26 identified in the Sulu Sea, 11 are unvegetated sand cays, 10 have sparse vegetation, and 5 are densely vegetated. Of the 16 reef islands in the Celebes Sea, 8 are sparsely vegetated, and 6 are densely vegetated. In the South China Sea, the densely vegetated Kalampunian Besar Island in the Pulau Tiga Park is contrasted with the extensive infrastructure of Pulau Layang-Layang Atoll. Many undeveloped islands occur in the Sulu Sea, while the three most developed islands occur in the Celebes Sea. Some islands, such as Mabul Island, are predominantly covered with buildings with construction extending over the reef flat. Several islands have been designated as Marine Protected Areas due to the significance of their biota. This inventory provides a baseline of the characteristics of these islands at the time of image acquisition to provide a much-needed record of their current status and against which future changes can be assessed. </p>