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Presented here are the supplemental data of the research article “Urinary pteridines as a discriminator of atherosclerotic risk in patients with diabetes” [1]. These data provide the first information on variables that affect urinary levels of pteridines (oxidized-form pteridine derivatives) in patients with diabetes mellitus. In linear regression analysis, gender (women vs. men), current history of smoking and urinary albumin showed significant positive correlations with pteridines, while there were significant inverse correlations of pteridines with a history of alcohol drinking and body mass index. The above associations were confirmed by using analysis of covariance and logistic regression analysis. Among the eight variables (age, gender, medication therapy for diabetes, smoking, alcohol drinking, body mass index, hemoglobin A1c and urinary albumin) tested, smoking showed the strongest association with urinary pteridines.