Previous studies have demonstrated an inverse correlation between the degree of respiratory drive and NHE3 mRNA expression in the brainstem of awake rabbits. Here we show that the levels of NHE3 mRNA extractable from kryo-conserved tissue are highly variable also in the human brainstem. As an insufficient drive to breath may be a final event causing sudden infant death, we compared the expression of NHE3 mRNA in a collective of children who died from non-natural causes to an equal number of SIDS victims. Evaluation of signals from NHE3 RT-PCR showed higher values for the SIDS collective than for the control group. We suggest that the level of NHE3 expression in brainstem tissue may contribute to the vulnerability of infants for SIDS.