<b><i>Background:</i></b> Gonadotrophin-releasing hormone (GnRH) antagonists reduce ovarian hyperstimulation syndrome (OHSS) at the price of a small reduction in effectiveness compared to GnRH agonists. The aim of this study was to investigate patients' preferences on effectiveness, safety and burden of GnRH analogs. <b><i>Methods:</i></b> A discrete choice experiment (DCE) and a trade-off question were designed. Patients embarking on assisted reproductive technique treatment were asked to choose between two hypothetical medications which differed in effectiveness, safety and burden. <b><i>Results:</i></b> A total of 172 questionnaires were analyzed. All attributes of the DCE had a statistically significant impact on the preference of the respondents. Respondents were willing to trade off 0.87 and 0.81% effectiveness for a decrease in OHSS risk and for fewer side effects, respectively. Respondents were not willing to trade off effectiveness for ‘importance of compliance' (trade-off 0.40%) or a shorter ‘duration of treatment' (trade-off 0.26%). The trade-off questions showed that already at a 2.0% increase in pregnancy rate in favor of the agonists, the majority of the respondents changed their preference from antagonists to agonists (2.0%, 95% CI 1.7-2.1). <b><i>Conclusion:</i></b> Safety and burden are important to patients, but are not important enough to make up for a small decrease in pregnancy rate.