Prenatal nicotine exposure influences neuronal development including effects on several neurotransmitter systems. It also attenuates the ventilatory response to hypoxia, known to require a functional substance P-ergic system. Previous studies have shown that nicotine increases the risk for sudden infant death syndrome (SIDS) by 4-fold, and that SIDS-victims have elevated brainstem levels of substance P. We, therefore, studied the effect of prenatal nicotine exposure on the levels of substance P-like immunoreactivity by RIA in the brain in newborn rat pups. The expression of the substance P precursor preprotachykinin A mRNA was also determined by real-time reverse transcriptase-polymerase chain reaction in carotid body, in petrosal/jugular and trigeminal ganglia, in cervical and lumbar dorsal root ganglia, and in the brainstem. We found that prenatal nicotine exposure increased levels of substance P-like immunoreactivity in the brainstem without changing levels in other parts of the brain or in the adrenals. Furthermore, mRNA levels were increased in the carotid bodies and in the petrosal ganglia, in contrast to the decreased levels in the cervical dorsal root ganglia. We conclude that nicotine causes alterations in the substance P-ergic system in the brainstem, possibly linked to the increased risk for SIDS after prenatal nicotine exposure.