Endometriosis is a chronic inflammatory gynaecological disease. Problems associated with endometriosis include dysmenorrhoea, dyspareunia and infertility. We evaluated the omega-3 and fatty acid profiles in erythrocytes and tissues in patients with endometriosis (n = 10) or a functional ovarian cyst (n = 12), using a food frequency questionnaire that included questions about 117 food items typical of Korean meals. Erythrocyte levels of 20:5n3 and 22:6n3, the omega-3 index, and n-3 PUFA were significantly higher, and the n-6:n-3 ratio was significantly lower in the endometriosis group than in the functional ovarian cyst group. The functional ovarian cyst group consumed significantly more fruit than the group with endometriosis.