In-vitro fertilization (IVF) procedures are effective in improving fertility in many women with endometriosis. IVF makes it possible to combine sperm and eggs in a laboratory and then place the resulting embryos into the woman's uterus. The decision when to apply IVF in endometriosis-associated infertility cases takes into account the age of the patient, the severity of the endometriosis, the presence of other infertility factors, and the results and duration of past treatments. In ovarian hyperstimulation as part of IVF in women with endometriosis, using a standard GnRH agonist protocol has been found to be equally effective in regard to using a GnRH antagonist protocol in terms of pregnancy rate. On the other hand, when using a GnRH agonist protocol, long-term (three to six months) pituitary down-regulation before IVF for women with endometriosis has been estimated to increase the odds of clinical pregnancy by fourfold. No difference has been found between surgery (cystectomy or aspiration) versus expectant management, or between ablation versus cystectomy, prior to IVF in women with endometriosis The mechanisms by which endometriosis may cause infertility are not clearly understood, particularly when the extent of endometriosis is low. Still possible mechanisms include: Anatomical distortions and adhesions (the fibrous bands that form between tissues and organs following recovery from an injury)The release of factors from endometriotic cysts which are detrimental to gametes or embryos. An endometriotic cyst contains free iron, reactive oxygen species, proteolytic enzymes and inflammatory molecules. Follicular density in tissue surrounding the endometriotic cyst has been consistently shown to be significantly lower than in healthy ovaries, and to a degree that does not appear to be caused merely by the stretching of surrounding tissues owing to the presence of a cyst. The other way around, endometriosis may more likely develop in women who fail to conceive for other reasons and thus be a secondary phenomenon. For this reason it is preferable to speak of "endometriosis-associated infertility" rather than any definite "infertility caused by endometriosis" by the same reason that association does not imply causation.

Primary infertility is defined as the absence of a live birth for women who desire a child and have been in a union for at least 12 months, during which they have not used any contraceptives. The World Health Organisation also adds that 'women whose pregnancy spontaneously miscarries, or whose pregnancy results in a still born child, without ever having had a live birth would present with primarily infertility'. Secondary infertility is defined as the absence of a live birth for women who desire a child and have been in a union for at least 12 months since their last live birth, during which they did not use any contraceptives.  Thus the distinguishing feature is whether or not the couple have ever had a pregnancy which led to a live birth.

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