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Background: Thiols are scavengers of reactive oxygen species (ROS). We aim to investigate associations between thiols in various fluids in (sub)fertile couples and fertility outcome parameters. Methods: In 156 couples undergoing assisted reproduction techniques (ART), we measured the concentrations of glutathione (GSH), cysteine (Cys), homocysteine (Hcy) and cysteinylglycine (CGS) and fertility outcome parameters in the ejaculate, purified spermatozoa and follicular fluid. Results: All thiols were detectable in most ejaculates, spermatozoa and follicular fluids, of which Cys concentrations were highest. Thiol concentrations in the ejaculate were similar in fertile and subfertile men. However, Hcy in follicular fluid was higher in women with endometriosis compared with women in the idiopathic subfertile group (P = 0.04). The GSH, Cys, Hcy and CGS concentrations in spermatozoa of subfertile men were significantly higher compared with men in the idiopathic subfertile group and fertile men (P < 0.001). Most notably, Hcy concentrations in both the ejaculate and follicular fluid were negatively associated with embryo quality on culture day 3 in the IVF/ICSI procedure. Conclusions: Spermatozoa of subfertile men contain significantly higher thiol concentrations as compared with those of fertile men. The detrimental effect on embryo quality of a high Hcy concentration in the ejaculate and in follicular fluid is intriguing and may suggest that Hcy is inversely associated with fertility outcome.