Optical projection tomography (OPT) is a new technique for three-dimensional (3D) imaging of small biological tissues. It is particularly useful for reconstructing vertebrate embryos and for examining the 3D anatomy of developing organs. The advantages of this technique over previous methods will be explained: in particular, its ability to image at a higher resolution than magnetic resonance imaging (MRI), while at the same time being able to image specimens much larger than those possible using confocal laser-scanning microscopy. Being an optical technique, OPT is also able to take advantage of the many coloured and fluorescent dyes which have been developed for tissue-specific or gene-specific staining. This becomes particularly important for the visualization of the 3D shapes of specific organs and tissues as it allows the computer to automatically determine the outline of the desired structure.