Endometriosis is a chronic inflammatory condition affecting up to 10% of women of reproductive age and this, depending on its severity, very often leads to infertility. New research has shed light on the role of underlying endometritis due to the presence of inflammatory, non-oestrogen metabolising microbiome at the mucosal interface and this in turn leads to the activation of aggressive, non-tolerant immune cells in the endometrium. These immune cells require the presence of tolerance-inducing commensals such as Lactobacilli so as to allow the implantation of the fertilised egg. New therapies should be holistic and address both the dysbiosis as well as immune abnormalities. Routine immune monitoring of the immune cells derived from the endometrium and/or microbial profiling should recommended to better predict assisted reproduction outcomes in these couples.