Background Ca2+in the central nervous system plays important roles in brain physiology, including neuronal survival and regeneration in rats with injured facial motoneurons. The present research was to study the modulations of intracellular free Ca2+ concentrations by cholinergic receptors in rat facial nucleus, and the mechanisms of the modulations. Methods The fluorescence intensity of facial nucleus in Fluo-3 AM loaded acute brainstem slices was detected by applying intracellular free Ca2+ measurement technique via confocal laser scanning microscope. The changes of fluorescence intensity of facial nucleus indicate the average changes of intracellular free Ca2+ levels of the neurons. Results Acetylcholine was effective at increasing the fluorescence intensity of facial nucleus. Muscarine chlorlde induced a marked increase of fluorescence intensity in a concentration dependent fashion. The enhancement of fluorescence intensity by muscarine chloride was significantly reduced by thapsigargin (depletor of intracellular Ca2+ store; P<0.01), rather than Ca2+ free artifical cerebrospinal fluid or EGTA (free Ca2+ chelator; P>0.05). And the increase of fluorescence intensity was also significantly inhibited by pirenzepine (M1 subtype selective antagonist; P<0.01) and 4-DAMP (M3 subtype selective antagonist; P<0.01). In addition, fluorescence intensity was markedly increased by nicotine. The enhancement of fluorescence intensity by nicotine was significantly reduced by EGTA, nifedipine (L-type voltage-gated Ca2+ channel blocker), dihydro-β-erythroidine (α4β2 subtype selective antagonist), and in Ca2+ free artificial cerebrospinal fluid (P<0.01), but not in the presence of mibefradil (M-type voltage-gated Ca2+ channel blocker) or thapsigargin (P>0.05).Conclusions The data provide the evidence that muscarinic receptors may induce the increase of intracellular free Ca2+ levels through the Ca2+ release of intracellular Ca2+ stores, in a manner related to M1 and M3 subtypes of muscarinic receptors in rat facial nucleus. Nicotine may increase intracellular free Ca2+ concentrations via the influx of extracellular Ca2+ mainly across L-type voltage-gated Ca2+ channels, in a manner related to the α4β2 subtype of nicotinic receptors.