The endometrium is one of the most fascinating tissues in the human body. Its sole purpose is to enable implantation of an embryo during a very short window of opportunity in the menstrual cycle. When implantation does not take place, the endometrial cells are shed, enabling growth of a new endometrial layer the following month. Recently recognized stem cells may be the source through which this physiological turnover can take place. These cells, however, may also result in pathological conditions such as endometriosis, adenomyosis and carcinoma when control by surrounding niche cells is lost. The methods to obtain endometrial tissue are critically reviewed, including the various catheters compared with the Pipelle. Recent advances in molecular studies of the endometrium enable researchers to define markers of implantation, and study the interaction between the embryo and the endometrium in vitro. Moreover, mechanisms by which wounding the endometrium by the biopsy catheter actually seems to improve embryo implantation are hypothesized. Finally, detection, isolation and differentiation of adult endometrial stem cells have the potential to provide a resource for therapy of chronic conditions.