Endometriosis is a common gynaecological disease where “endometrial-like” tissue forms ectopic lesions, most commonly in the pelvis. The disease affects 11% of reproductive-aged women within their lifetime, and presents with a range of symptoms, often including pelvic pain. Surgical and medical treatments aimed at reducing symptoms can have limited effectiveness, side effects and patient-to-patient variability. While some patients respond well to treatment there is no ‘one shoe fits all’ approach to managing endometriosis. Endometriotic lesions are the characteristic feature diagnostic of endometriosis and variable macroscopic and microscopic lesion appearances have been observed. Despite this heterogeneity, features beyond the presence/absence of endometrial-like glands and/or stroma are not factored into diagnosis. Additionally, existing endometriosis classification systems are based on surgical observations and do not predict treatment responsiveness or disease prognosis. This is unlike other pathologies (e.g. gynaecological cancers) where an array of disease characteristics are factored in to diagnosis to guide treatment decisions and predict outcomes. The identification of distinct endometriotic lesion subtypes that relate to clinical outcomes would be invaluable to improving treatment for endometriosis patients. The objective of this thesis was to characterise specific microscopic features of superficial peritoneal endometriotic lesions including histological and immunohistochemical characteristics such as collagen, smooth muscle, leukocytes, steroid receptors, proliferative markers, innervation, and vasculature. Studies aimed to determine if distinct subtypes of lesions exist based on these features. These studies also aimed to determine if endometriotic lesions exhibit patterns in these features based on menstrual cycle phase and if these patterns reflected those of matched eutopic endometrium. Based on the histological features and tissue and cell types ana