Objective To study the preferences and risk tolerance of women suffering from deep endometriosis (DE) with bowel involvement when they have to choose between conservative or surgical. Design Labelled Discrete Choice Experiment (DCE). Setting Dutch academic and non-academic hospitals and online recruitment. Population or Sample A total of 169 patients diagnosed with DE of the bowel. Methods Baseline characteristics and the fear for surgery were collected. Women were asked to rank attributes and choose between hypothetical conservative (medication) or surgical treatment in different choice sets (scenarios). Each choice set offered different levels of all treatment attributes. Data were analysed by using multinomial logistic regression. Main Outcome Measures The following attributes; effect/or risk on pain, fatigue, pregnancy, endometriosis lesions, mood swings, osteoporosis, temporary stoma and permanent intestinal symptoms were used in this DCE. Results In the ranking osteoporosis is the least important attribute, while in the DCE, a lower chance of osteoporosis is one of the most important drivers when choosing a conservative treatment. Women with previous surgery show less fear for surgery compared to women without surgery. The low anterior resection syndrome is almost equally important for patients as the chance of pain reduction. Pain reduction has higher importance than improving fertility chances even in women with a future child wish. Conclusions The risk of suffering from LARS as a result of treatment is almost equally important as the reduction of pain symptoms. Women with previous surgery experience less fear for surgery compared to women without a surgical history.