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To assess the relationship between urinary fluoride and micronutrients intake we recruited 121 schoolchildren from San Luis Potosí. We evaluated fluoride concentrations in drinking water and urine with the ion-selective electrode method and estimated calcium, magnesium, and phosphorus intakes with a validated consumption frequency questionnaire. About 72% of the population used tap water for drinking and cooking. Fluoride concentrations were 2.36 ± 0.02 mg/L in tap water, 0.14 ± 0.04 mg/L in bottled water and 2.05 ± 0.62 mg/L in urine. Urinary fluoride was higher in children with a consumption <50% of the Recommended Daily Intake (RDI) of calcium (2.20 v/s 1.96 mg/L; p < 0.05), <50% RDI of magnesium (2.58 v/s 1.96 and 1.90 mg/L; p < 0.05) and >150% RDI of phosphorus (2.43 v/s 1.82 mg/L; p < 0.05). These data indicated that fluoride concentration in tap water is higher than bottled water and estimated micronutrients intake is related to urinary fluoride.