In recent years anti-doping organizations have implemented various measures to deter elite athletes from using performance-enhancing drugs. One of the main challenges in the fight against doping is that the effectiveness of these anti-doping measures is still unknown. Since the effectiveness of the measures depends primarily on the athletes’ perception, this study focuses on the following four objectives: (1) How effective do top-level athletes perceive individual anti-doping measures to be? (2) Are the results stable across different sports and (3) genders? (4) How can the anti-doping measures be structured into appropriate categories? To address these issues the perceived effectiveness of 14 anti-doping measures was surveyed among 146 top athletes from Germany (Cycling: N = 42; Athletics: N = 104) who are members of at least the National Testing Pool. Results reveal significant differences in the perceived effectiveness of the anti-doping measures. Improved diagnostics were considered to be the most effective remedy for doping, followed by increased bans and the implementation of an anti-doping law. In contrast, fines and a leniency program were considered significantly less effective. Second, with the exception of indirect detection methods and increased use of an Anti-Doping Administration and Management System, results were consistent across cyclists and track and field athletes. Third, no significant gender difference was observed. Finally, an exploratory factor analysis showed that all anti-doping measures can be classified into the three categories risk of detection (e.g., control frequency and efficiency), punishment (e.g., fines and bans) and communication (e.g., education program). The results of this study provide a guideline for future research and for anti-doping and sport organizations when developing strategies against doping and allocating their anti-doping budget.