Since the stomach lacks a well-developed ganglionated submucous plexus, the somata of enteric neurones innervating the muscle or the mucosa have to be localised within the myenteric plexus. The aim of this study was to determine the projection pathways and the neurochemical coding of myenteric neurones innervating these different targets in the gastric fundus. Myenteric cell bodies projecting to the mucosa or the circular muscle were retrogradely labelled by mucosa or muscle application of the fluorescent tracer DiI and subsequently characterised by their immunoreactivity for choline acetyltransferase (ChAT), nitric oxide synthase (NOS), substance P (SP) and/or neuropeptide Y (NPY). On average 14391 and 8949 myenteric neurones were labelled from the mucosa and the circular muscle, respectively. DiI-labelled neurones were either ChAT-or NOS-positive. DiI-labelled ChAT-positive neurones were mainly ascending and outnumbered NOS-positive neurones, which were mainly descending (79.36.2% vs 20.76.2% for mucosa neurones; 69.311.1% vs 30.711.1% for muscle neurones). Three ChAT-positive subpopulations (ChAT/±, ChAT/SP, ChAT/NPY) and two NOS-positive subpopulations (NOS/±, NOS/NPY) were found. ChAT/SP neurones projected mainly to the circular muscle (36.111.9% of the cholinergic muscle neurones; mucosa projection: 8.02.1%), whereas ChAT/NPY neurones projected mainly to the mucosa (38.19.2% of the cholinergic mucosa neurones; muscle projection: 5.72.4%). NOS/± cells projected predominantly to the muscle. This study demonstrates polarised pathways in the myenteric plexus consisting of ascending ChAT and descending NOS cells that innervate the circular muscle and the mucosa of the gastric fundus. The ChAT/SP neurones might function as circular muscle motor neurones, whereas ChAT/NPY neurones might represent secretomotor neurones.