Abstract Inhibitory axosomatic synapses could effectively suppress the excitability of postsynaptic cells. It is important to examine the development of inhibitory axosomatic synapses to understand the maturation of information processing. The caudal nucleus tractus solitarius (cNTS), which regulates the autonomic system, consists of several subnuclei. In the present study, development of axosomatic synapses in the dorsal and ventral subnuclei was examined by electron microscopy. In dorsal subnuclei, the percentage of GAD-positive terminals on the somata, the percentage of small cell somata with synapses and axosomatic synapse density drastically decreased from postnatal day (P) 5 to P10. In ventral subnuclei, the percentage of GAD-positive terminals on the soma, the percentage of small or large cell somata with synapses and axosomatic synapse density were maintained or increased from P5 to P10. Thus, decrease of inhibitory axosomatic synapses in dorsal subnuclei might facilitate maturation of fine receptive areas for peripheral inputs, while increase of inhibitory axosomatic synapses in ventral subnuclei might facilitate the establishment of an effective regulation system for cNTS output.