In the gastrointestinal (GI) tract of mammals, endings of spinal afferent neurons with cell bodies in dorsal root ganglia (DRG) detect many stimuli, including those that give rise to pain. Many of these sensory neurons express calcitonin gene-related peptide (CGRP) and TRPV1 in their cell bodies and axons. Indeed, CGRP and TRPV1 have been widely used as immunohistochemical markers of nociceptive spinal afferent axons. Although CGRP and TRPV1 often coexist in the same axons in the GI tract, their degree of coexistence along its length has yet to be quantified. In this study, we used double-labeling immunohistochemistry to quantify the coexistence of CGRP and TRPV1 in varicose axons of the murine oesophagus, stomach and colorectum. The great majority of CGRP-immunoreactive (IR) varicosities in myenteric ganglia of the lower esophagus (97 ± 1%) and stomach (95 ± 1%) were also TRPV1-immunoreactive. Similarly, the majority of TRPV1-IR varicosities in myenteric ganglia of the lower esophagus (95 ± 1%) and stomach (91 ± 1%) were also CGRP-IR. In the colorectum similar observations were made for an intensely immunoreactive population of CGRP-IR axons, of which most (91 ± 1%) were also TRPV1-IR. Of the TRPV1-IR axons in the colorectum, most (96 ± 1%) contained intense CGRP-IR. Another population of axons in myenteric ganglia of the colorectum had low intensity CGRP immunoreactivity; these showed negligible co-existence with TRPV1. Our observations reveal that in the myenteric plexus of murine oesophagus, stomach and colorectum, CGRP and TRPV1 are largely expressed together.