On the basis of measurements on fresh human brains (n = 33), changes in size of the brain stem which occurred as a result of formalin fixation and embedding in paraffin were quantified and converted into linear correction factors. In contrast to the known changes in the cerebrum, the formalin fixation did not result in a 'positive formalin effect', but left transverse values unchanged and led to decreases in longitudinal distances of 1-8% (correction factors: 1.01-1.09). Further embedding resulted in a linear shrinkage of 11-12% (correction factors: 1.12-1.13) transversely and 17% (correction factor: 1.21) longitudinally, which was smaller than the shrinkage in the cerebrum of 11-25% (correction factors: 1.13-1.34) reported in the literature. The examinations revealed changes in the brain stem caused by the total fixation and embedding process different from those of the cerebrum.