AIM: The outstanding performance of elite athletes is a product of a complex interaction between genetic and environmental factors. The aims of this study was to compare differences in genetic and metabolic profiles among different classes of elite athletes and to identify genetically-influenced metabolic profiles (metabotypes) underlying these differences. METHODS: Genome-wide association study (GWAS) was conducted in 1259 elite athlete samples using Drug core BeadChip arrays, followed by non-targeted metabolomics of 692 serum samples. Genotype distribution, differences in metabolic levels and genetically-influenced metabotypes were compared between high and moderate endurance and power sports as well as among sports with different cardiovascular demands (CVD). RESULTS: Out of 341385 SNPs, two novel associations are reported for endurance status including rs56330321 in ATP2B2 (p=1.47E-7) and rs2635438 in SYNE1 (p=2.54E-7). A meta-analysis confirmed the association of rs56330321 and rs2635438 with endurance athlete status at GWAS level of significance. Metabolomics analysis of 740 metabolites was performed in in 191 (discovery cohort) and 500 (replication cohort) elite athletes. These studies revealed changes in various metabolites involved in steroid biosynthesis, fatty acid oxidation, oxidative stress response, xenobiotics and various mediators of cell signaling among different groups of endurance, power and CVD athletes. By combining GWAS with metabolomics profiling data (mGWAS), 19 common variant metabolic quantitative trait loci (mQTLs) were identified, of which 5 were novel. When focusing on metabolites associated with endurance, power and CVD, 4 common variant mQTLs were found, of which one novel mQTL linking 4-androsten-3alpha,17alpha-diol monosulfate and SULT2A1 involved in steroid sulfation was identified in association with endurance. CONCLUSIONS: GWAS, metabolomics and mGWAS of elite athletes identified novel markers associated with elite athletic performance with a potential application in biomarker discovery in relation to elite athletic performance.