Low QRS voltages (LQRSV) in limb leads and QRS fragmentation (FQRS) are possible electrocardiographic signs of myocardial fibrosis and cardiomyopathy, but they are not listed in current criteria for interpreting athlete's electrocardiogram (ECG). We investigated the prevalence and determinants of LQRSV and FQRS in a cohort of young apparently healthy athletes undergoing pre-participation screening (PPS). We analysed a consecutive series of 2140 ECG obtained during PPS of young athletes (mean age 12.5 ± 2.6 years, 7-18-year-old, 49% males). The peak-to-peak QRS voltage was measured in all limb leads, and LQRSV were defined when maximum value was <0.5 mV. Fragmented QRS morphologies were grouped into five patterns. Lead aVR was not considered. Maximum peak-to-peak QRS voltage in limb leads was 1.4 ± 0.4 mV, similar between younger and older athletes, but significantly lower in females than males (1.35 ± 0.38 mV vs. 1.45 ± 0.42 mV; P < 0.001). There was a weak correlation between maximal QRS voltages and body mass index (BMI), but not with type of sport or training load. Only five (0.2%) individuals showed LQRSV. At least one fragmented QRS complex was identified in 831 (39%) individuals but excluding the rSr' pattern in V1-V2, only 10 (0.5%) showed FQRS in ≥2 contiguous leads. They were older than those without FQRS, but did not differ in terms of gender, BMI, type of sport, or training load. Low QRS voltages in limb leads and FQRS in ≥2 contiguous leads excluding V1-V2 are rare in young apparently healthy athletes and are not related to the type and intensity of sport activity. Therefore, they may require additional testing to rule out an underlying disease particularly when other abnormalities are present.