We examined the distribution patterns and axonal pathways of cholinergic, GABAergic, and dopaminergic neurons in the central nervous system of Ciona intestinalis larvae, based on the expression patterns of two reporter genes (GFP and LacZ) driven by the promoters of several neuron-specific genes (vesicular acetylcholine transporter, glutamic acid decarboxylase, tyrosine 3-hydroxylase and dopa decarboxylase). Putative cholinergic and GABAergic cells were found in the sensory vesicle (SV) and visceral ganglion (VG), while putative dopaminergic cells were found only in the SV. The axons of almost all putative cholinergic and GABAergic cells in the SV extend posteriorly towards the VG and seem to connect with motor neurons. Some cells extend axons to the proximal region of the tail beyond the trunk-tail boundary. As this tail region contains several neurons, these cells may modulate larval behavior through the latter neurons. We also found that some putative cholinergic and GABAergic cells in the dorsal VG form a complex and extend axons anteriorly to the SV, posteriorly to the tail, and possibly ventrally to some motor neurons. Finally, we observed that one pair of the anterior most putative cholinergic cells in the ventral VG extends axons contralaterally to the right and left caudal axon tracts. We discuss the similarity of these cells to the Mauthner cells in vertebrates.