Serotoninergic and cholinergic neurons are known to appear earlier in the ontogeny (day E12) of the murine gut than those containing substance P or vasoactive intestinal peptide (day E14). It has also been demonstrated that proliferating neural precursors coexist with mature neurons in developing enteric ganglia. These observations have led to the hypotheses that peptidergic neurons develop later than those that utilize small molecule neurotransmitters and that the activity of early developing neurons may affect the phenotypic expression of coexisting neuroblasts. As a partial test of these hypotheses we studied the phenotypic expression of neurons recognized by antisera to neuropeptide Y (NPY) and calcitonin gene-related peptide (CGRP), and of those visualized by the histochemical demonstration of reduced nicotinamide adenine dinucleotide phosphate (NADPH) diaphorase activity. NADPH diaphorase activity, which is coexpressed with NPY immunoreactivity in all submucosal and many myenteric neurons, was first found on day E11 in clusters of cells in the dorsal mesogastrium. These cells also expressed neurofilament reactivity and thus were developing along a neuronal lineage. Enteric neurons that expressed NADPH diaphorase activity were visualized in the stomach one day later, on day E12. At this time, NADPH diaphorase-containing cells could no longer be demonstrated in the dorsal mesogastrium. NPY immunoreactivity first appeared in the wall of the bowel on day E12, when it was seen in cells in the presumptive stomach. By day E13, the entire length of the bowel contained NPY-immunoreactive neurons. Cells that displayed NADPH diaphorase activity were found at this time at both ends of the alimentary tract, but did not appear in the ileum until day E18. In contrast, CGRP immunoreactivity could not be detected anywhere in the gut until day E17, but by day E18 all regions of the bowel contained CGRP-immunoreactive neurons. Endogenous 5-HT was first detected at day E16 in mucosal epithelial cells in all segments of the gut except the stomach, where it appeared at day E18. The NPY/NADPH diaphorase set of neurons thus develop before the acquisition of a detectable level of endogenous 5-HT or enteric neural 5-HT receptors (which arise in the foregut at day E14). These observations demonstrate that enteric neurons that express small molecule neurotransmitters do not necessarily develop earlier than peptidergic neurons as a class; however, various types of enteric neurons do appear in a sequential order.(ABSTRACT TRUNCATED AT 400 WORDS)