The FTO A/T polymorphism (rs9939609) has been strongly associated with body mass-related traits in nonathletic populations, but rarely with elite athletic performance. The aim of the study was to investigate the association between the A/T polymorphism and athlete status in elite swimmers. Polish swimmers (n = 196) who competed in national and international competition at short- (SDS; 50–200 m; n = 147) and long-distance events (LDS; ≥400 m; n = 49) were recruited. The control group included 379 unrelated, sedentary young participants. The participants were all Caucasians. Genotyping was carried out using real-time PCR. It was found that the chance of being an elite swimmer was lower in carriers of the AT and AA genotype compared with TT homozygotes (1.5 and 2.0 times, respectively). These findings were confirmed in an allelic association; the A allele was less frequent in the swimmers compared with controls (p = 0.004). However, when SDS were compared against LDS, no significant differences were observed in genotypic and allelic distribution. The results of our experiment suggest that the variation within the FTO gene can affect elite athlete status. It was demonstrated that harboring the T allele may be beneficial for achieving success in a sport such as swimming.