Interstitial cells of Cajal (ICCs) are located in various smooth muscle organs and act as pacemaker cells, or ensure neuromodulation or mechanosensory roles. The study aims to investigate functional states of human ICCs in morphogenesis, focusing on the anoctamin 1 phenotype. The investigation was performed in five late stage human embryos with lengths varying between 23 and 29 mm. Immunohistochemistry on paraffin embedded specimens was performed for a series of antibodies: a-smooth muscle actin (a-SMA), desmin, CD31, CD34, CD117/c-kit, DOG1, and nestin. Longitudinal and circular muscle layers were a-SMA1/desmin1/nestin1. An immature microvascular layer located in the inner submucosa was CD341/CD311/a-SMA1/ nestin1; endothelial tip cells were supporting active processes of sprouting angiogenesis. A CD341/CD31- mesenchymal network was found in the circular muscle layer. CD117/c-kit1 multipolar ICCs with dichotomizing processes were found mostly in the myenteric plexus layer; processes were configuring a network within the circular muscle layer where intramuscular ICCs were scarcely found. A strong DOG11 reaction was found for the ICCs of the myenteric plexus layer apposed on the outer surface of the circular muscle layer, and for the intramuscular ICCs. The evidence of a sublayer of DOG11 myenteric ICCs is suggestive for a subpopulation of ICCs being qualified for pacemaking at this early developmental stage.