Although endometriosis has been known for over 100 years, its pathogenesis is still poorly understood. In this overview the literature regarding the pathogenesis of endometriosis is reviewed. The implantation or transplantation theory, that suggests implantation and subsequent growth of retrogradely shed viable endometrial cells, still remains the most widely accepted theory to explain the pathogenesis. The conditions that have to be met for the implantation theory are threefold: (i) retrograde menstruation has to occur; (ii) retrograde menstruation should contain viable endometrial cells; and (iii) adhesion to the peritoneum has to occur with subsequent implantation and proliferation. The scientific data to corroborate these conditions will be discussed. A short overview is given on cell adhesion molecules, in particular cadherins and integrins, the most important cell adhesion molecules involved in cell-cell adhesion and cell-extracellular matrix interaction. Special attention is given to the possible functional role of these cell adhesion molecules in the pathogenesis of endometriosis.