Endometriosis has a wide clinical spectrum and induces a chronic inflammatory process. The incidence of endometriosis in women with dysmenorrhoea is up to 40-60%, whereas in women with subfertility is up to 20-30%. Recurrence of endometriosis varies greatly among different studies. The overall recurrence rates range between 6 to 67% according to the criteria that are taken into consideration. Which of the various reasons is more predictive for recurrence is still unclear and controversial. The main aim of post-operative medical treatment is suppressing ovarian activity leading to atrophy of endometriotic lesions. The success of treatment depends on the resorption of all residual visible lesions and the eradication of microscopic implants. The recurrent lesions might originate from residual lesions or from de novo cells. Determining risk factors for recurrence may allow the identification of subgroups at risk for disease control. Potential biomarkers for recurrence could also maintain targeted therapy.