The total number of neurons in the medial and lateral habenular nuclei of the rat epithalamus was estimated using modern stereological counting methods and systematic random sampling techniques. Six to eight young adult male rats, and a complete set of serial 40-μm glycolmethacrylate sections for each rat, were used to quantify neuronal numbers. After a random start, a systematic subset (e.g. every third) of the serial sections was used to estimate the total volume of each nucleus using Cavalieri's method. The same set of sampled sections was used to estimate the number of neurons in a known subvolume (i.e. the numerical density Nv) by the optical disector method. Multiplication of the total volume by Nv yielded the total number of neurons. It was found that the right medial habenular nucleus consisted, on average, of 18 000 neurons (with a coefficient of variation of 0.18), while the right lateral habenular nucleus had 13 000 neurons on average (0.14). These total neuronal numbers provide important data for the transfer of information through these nuclei and for species comparisons.