Three-dimensional (3D), multiwavelength near-infrared tomography has the potential to provide new physiological information about biological tissue function and pathological transformation. Fast and reliable measurements of multiwavelength data from multiple planes over a region of interest, together with adequate model-based nonlinear image reconstruction, form the major components of successful estimation of internal optical properties of the region. These images can then be used to examine the concentration of chromophores such as hemoglobin, deoxyhemoglobin, water, and lipids that in turn can serve to identify and characterize abnormalities located deep within the domain. We introduce and discuss a 3D modeling method and image reconstruction algorithm that is currently in place. Reconstructed images of optical properties are presented from simulated data, measured phantoms, and clinical data acquired from a breast cancer patient. It is shown that, with a relatively fast 3D inversion algorithm, useful images of optical absorption and scatter can be calculated with good separation and localization in all cases. It is also shown that, by use of the calculated optical absorption over a range of wavelengths, the oxygen saturation distribution of a tissue under investigation can be deduced from oxygenated and deoxygenated hemoglobin maps. With this method the reconstructed tumor from the breast cancer patient was found to have a higher oxy-deoxy hemoglobin concentration and also a higher oxygen saturation level than the background, indicating a ductal carcinoma that corresponds well to histology findings.