Although there are a number of studies on policy making concerning doping and anti-doping in elite sports, the athletes’ perspective has largely been neglected. The present study contributes to bridging this gap. Since forming and developing the anti-doping policy utterly depends on how legitimate the practitioners believe this policy to be, the specific aim for this paper is to study how elite athletes at the broad international arena perceive the legitimacy of anti-doping policy and practices. An on-line questionnaire, designed to capture elite athletes’ perceptions, was answered by 261 respondents from 51 different countries and four international sports federations. Respondents were elite athletes belonging to the International Registered Testing Pool of each federation. The respondents were generally supportive towards anti-doping policy. Over 80% agreed that different anti-doping activities, from doping controls and the whereabouts system to storing of test samples and biological passports, are essential parts of the work against doping in sports. Support for anti-doping policy is also shown when 80% of the athletes agreed that anti-doping work should develop in a way that there is the same level of, or more, anti-doping activities compared to the current. The principle of anti-doping is, in this study, shown to be legitimate. However, at the level of practices, four areas were perceived as challenging. Regarding practical procedures, 34% experienced difficulties filing whereabouts information and 73% felt worried that they won’t be available for testing at the right place and right time in correlation to the whereabouts information they had provided. Concerning the athletes’ personal life and privacy, 50% of female athletes and 30% of males stated that they feel somewhat or very uncomfortable regarding their privacy when providing a urine sample. Furthermore, in regard to the whereabouts system, 47% of the respondents stated that they feel monitored. The efficacy and equality of anti-doping work is put under question by 58% who believed that users of forbidden substances/methods escape detection and 44% who did not believe that the whereabouts system is working properly in all countries. 70% of the respondents did not believe that all athletes applying for a therapeutic use exemption are treated in the same way. Regarding the athletes influence and participation in the policy work, 85% believe that athletes should be more involved. These four areas can be seen as unintended consequences of the work and reveal a weak point for the legitimacy of anti-doping when the athletes not fully perceive procedural justice. In conclusion, legitimacy for anti-doping policy in general is strong while a questioning of the legitimacy in the execution of the rules is discerned. If anti-doping authorities wish to maintain and increase the legitimacy of the anti-doping efforts, a thorough understanding for and consideration of the athletes’ perceptions is beneficial.