Abstract Background Sex-specific differences in nephrolithiasis with respect to both distribution of prevalence and stone composition are widely described and may be influenced by sex hormones. Methods We conducted a cross-sectional analysis of the relationship between 24-h urinary sex hormone metabolites measured by gas chromatography–mass spectrometry with urinary calcium, oxalate and citrate excretion in a cohort of 628 kidney stone formers from a tertiary care hospital in Switzerland, taking demographic characteristics, kidney function and dietary factors into account. Results We observed a positive association of urinary calcium with urinary testosterone and 17β-oestradiol. Positive associations of urinary calcium with dehydroepiandrosterone (DHEA), 5α-DH-testosterone, aetiocholanolone, androsterone and oestriol were modified by net gastrointestinal alkali absorption or urinary sulphate excretion. As the only sex hormone, DHEA was inversely associated with urinary oxalate excretion in adjusted analyses. Urinary citrate correlated positively with urinary testosterone. Associations of urinary citrate with urinary androsterone, 17β-oestradiol and oestriol were modified by urinary sulphate or sodium or by sex. Conclusions Urinary androgens and oestrogens are significantly associated with urinary calcium and citrate excretion and associations are modified in part by diet. Our data furthermore reveal DHEA as a novel factor associated with urinary oxalate excretion in humans.