A method of optically monitoring oxygen saturation of blood haemoglobin in the rat brain stem was developed. Optical fiber bundles were attached to the orifices of both ears of the rat to irradiate incident light from one ear and receive transmitted light from the other ear. Absorption spectra were measured using a white-light source and a photodiode array spectrophotometer. Stable measurements of optical time courses and absorption spectra were made using this "ear-to-ear" path. Oxygen saturation levels were calculated from spectra by using a suitable reference and an improved method of determining spectral peak heights.