INM is the apicobasal (AB) cell polarity-based oscillatory movement of epithelial cell nuclei in synchrony with the cell cycle, and is suggested to be involved in of the development of epithelial tubular organs.  Here, we investigated inter-organ (trachea vs. esophagus) and intra-organ regional (ventral vs. dorsal) differences in the INM mode in the tracheal and esophageal epithelia of the mouse embryo. The pregnant mice received a single intraperitoneal injection of 5-ethynyl-2’-deoxyuridine (EdU) at embryonic day (E) 11.5 and E12.5 and embryos were obtained 1, 4, 6, 8 and 12 hr later. The labeled cell nuclei distribution along the AB axis was chronologically analyzed in the total, ventral and dorsal sides of the epithelia. The percentage distribution of the nuclei population was represented by histogram and the chronological change was analyzed statistically using multi-dimensional scaling. The inter-organ comparison of the INM mode during E11.5-E12.0, but not E12.5-E13.0, showed a significant difference. During E11.5-E12.0 the trachea, but not the esophagus, showed a significant difference between ventral and dorsal sides. During E12.5-E13.0 neither organ showed regional differences. These findings indicate the existence of different modes of INM between the two organs which derive from the common anterior foregut as well as between the dorsal and ventral sides of the trachea. These differences in the INM mode may be related with the later differential organogenesis/histogenesis between the two organs as well as between the dorsal and ventral sides of the trachea.