To determine whether urine cobalt (Co) is associated with the prevalence of kidney stones, we conducted a cross-sectional study of participants (≥ 20 years) involved in the National Health and Nutrition Examination Survey (NHANES) between 2007 and 2018. The urine Co level was divided into four groups: 0.02-0.22, 0.22-0.36, 0.36-0.58, and 0.58-37.40 μg/L. The independent correlation between urine Co and prevalence of kidney stones was determined by logistic regression analyses. A total of 10,744 participants aged over 20 years that were not pregnant were eligible. Among them, 1041 participants reported ever having developed kidney stones. Patients with kidney stones developed significantly higher urine Co than the non-stone participants. The kidney stone patients were more likely to have been smoking ≥ 100 cigarettes in life; have hypertension, diabetes, and cancer; and engage in heavy activity. Multivariate logistic regression indicated a significantly positive relationship between the urine Co level and occurrence of kidney stones (OR 1.059, 95% CI 1.018-1.102, P = 0.00430). Moreover, the outcome remained unchanged after some sophisticated factors were adjusted (OR 1.059, 95% CI 1.001-1.120, P = 0.04635), and kidney stones were significantly related to a higher level of Co (OR (95% CI) = 0.22-0.36 μg/L: 1.111 (0.869, 1.421); 0.36-0.58 μg/L: 1.392 (1.095, 1.770); 0.58-37.40 μg/L: 1.712 (1.351, 2.170), and P for trend < 0.00001). So, urine Co concentration is positively associated with the prevalence of kidney stones. However, more high-quality prospective studies are needed to elucidate the causal correlation between Co level and kidney stones.© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.