An optical tomography system is developed for generating three-dimensional reconstructions of thick objects from projections. The system is useful for studying transparent structures that are 1-10 mm in diameter. Evaluation of the reconstruction system with a test object demonstrates 98% geometric accuracy, 90% accuracy in the detection of boundaries, and 90% accuracy in the measurement of absorbance. Reconstructions are computed from 96 parallel projections spaced evenly within 180 degrees . Accurate alignment of the projections is achieved with a cross-correlation method following data acquisition. Application of the optical tomography reconstruction technique to an intact cochlea permits measurement of internal structures with 16-microm pixels and a diffraction-limited resolution of 24 microm.