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Metabolomics is the systematic study of metabolites as small-molecule biomarkers that represent the functional phenotype in a cell, tissue or organism. Detection of crucial disturbances in the concentration of metabolites by metabolomic profiling of key biomarkers can be beneficial in the management of various medical conditions, including male-factor infertility. Recent studies have demonstrated the potential role of this rapid, noninvasive analysis in the investigation of infertile men. Differences in the concentration of oxidative stress biomarkers (–CH, –NH, –OH and ROH) have been found to be uniquely associated with semen plasma of healthy men compared with patients with idiopathic infertility, varicocele and vasectomy reversal. Furthermore, NMR spectra have shown significant differences in citrate, lactate, glycerylphosphorylcholine and glycerylphosphorylethanolamine among semen samples of men with spermatogenesis failure, obstructive azoospermia, oligoasthenoteratozoospermia and healthy donors. Evidence has also shown the value of 31P-magnetic resonance spectroscopy in differentiating patients with testicular failure and ductal obstruction by utilizing phosphomonoester and β-adenosine triphosphate as biomarkers. In addition, metabolomics has shown promise in assisted reproductive techniques. Recent studies involving spectroscopic measurements of follicular fluid and embryo culture media have revealed an association between biomarkers of oxidative stress and pregnancy outcome of oocytes and embryos.