A common single nucleotide polymorphism in the ACTN3 gene might result in the complete deficiency of α-actinin-3 (i.e., XX genotype). It has been found that ACTN3 XX individuals have several traits related to lessened muscle performance. This study aimed to determine the influence, if any, of ACTN3 genotypes on injury incidence of marathoners during the year preceding to participating in a competitive marathon race. Using a cross-sectional experimental design, the type and conditions of sports injuries were documented for one year in a group of 139 marathoners. Injuries were recorded following a consensus statement on injuries in Athletics. Afterward, ACTN3 genotyping was performed, and injury epidemiology was compared among RR, RX, and XX genotypes. The distribution of the RR/RX/XX genotypes was 28.8/42.8/23.5%, respectively. A total of 67 injuries were recorded. The frequency of marathoners that reported any injury during the previous year was not different across the genotypes (55.0/38.8/40.6%, P = 0.241). Although the overall injury incidence was not different among genotypes (2.78/1.65/1.94 injuries/1000 h of running, P = 0.084), the likelihood of suffering an injury was higher in RR than in RX (OR = 1.93: 95%CI = 0.87-4.30), and higher than in XX (OR = 1.79: 0.70-4.58). There was no difference in the conditions, severity, body location, time of year, or leading cause of injury among genotypes. However, XX presented a higher frequency of sudden-onset injuries (P = 0.024), and the OR for muscle-type injuries was 2.0 (0.51-7.79) times higher compared to RR runners. Although XX marathoners did not have a higher overall incidence of injury, the OR in these runners for muscle-type injuries was superior to RR and RX runners. The likelihood of suffering a muscle injury, especially with a sudden-onset, was twice in XX than in RR endurance runners.