The ectopic endometrial tissues lining the lumen of the fallopian tubes are currently defined as either “endometrial colonization” or “endometriosis” on the basis of their location within or beyond the isthmic portion of the fallopian tubes. The underlying etiology is unclear. The goal of this study was to define the fallopian endometrial lesions pathogenetically rather than anatomically. We investigated 39 cases of the ectopic endometrial tissues within the fallopian tubes, most of which exceeded the isthmus. Immunohistochemical analysis was performed to evaluate the expression of Cox-2, NF-κB, and VEGF, which are specifically expressed by classic endometriosis. Other clinicopathologic parameters were also recorded. The results indicated that the lesions that were confined to the mucosa might differ from those observed in the muscular or serosal layers, which showed significantly less surrounding inflammatory reaction and less concurrent salpingitis and other endometriotic lesions. The expression of Cox-2, NF-κB, and VEGF of the ectopic endometrial stromal cells tended to increase in the progression from the inner to the outer part of the tubes with significance. The expression of NF-κB and VEGF correlates with the microscopic findings of inflammation. Sterilization by tubal ligation exhibited a unique pattern of distribution. Except in those patients with tubal ligation, considering the different expression patterns observed in the tubal ectopic endometrial lesions, the mucosal type should be diagnosed as “endometrial colonization” wherever the lesion occurs. The others should be diagnosed as “endometriosis” to reveal the etiology identical to typical endometriotic lesions.