Objective: To study the experiences, considerations, and motivations of patients with endometriosis in the decision-making process for deep endometriosis (DE) treatment options. Design: Qualitative study using semi-structured in-depth focus group methodology. Setting: University medical center. Patient(s): A total of 19 Dutch women diagnosed with DE between 27 and 47 years of age. Intervention(s): Not applicable. Main Outcome Measure(s): Focus group topics were disease impact and motives for treatment, expectations of the treatment process, and important factors in the decision process. Result(s): Women reported that pain, fertility, and strong fear of complications are important decisive factors in the treatment process. The goal of conceiving a child is considered important, however, sometimes doctors emphasize this topic too much. It emerged that complication counseling is frequently about surgical complications, whereas side effects of hormonal treatments are neglected. Shared decision making and information about treatment options, complications, and side effects are not always optimal, making it difficult to make a well-considered choice. Despite negative experiences encountered after surgery, the positive effect of surgery ensures that most women do not regret their choice. Conclusion(s): In the treatment decision process for patients with DE, pain is almost always the most important decisive factor. The wish to conceive and strong fear of complications can change this choice. Doctors should understand the importance of fertility for the majority of women, but, also, if this is not considered paramount, respect that view. To improve shared decision making, exploration of treatment goals, training of healthcare providers, and better patient information provision are desirable.