The use of fingernails and urine as biomarkers of exposure to fluoride (F) from fluoridated dentifrice and varnish was evaluated in twenty 4- to 7-year-old children, who were divided into two groups: group A (9 caries-free children) and group B (11 children with past caries experience). They used a placebo dentifrice for 28 days, fluoridated dentifrice (1,570 ppm F) for the following 28 days, and placebo dentifrice for an additional 28 days, then returned to their usual dentifrices. Group B children also received 4-week applications of a varnish (2.26% F) while using the fluoridated dentifrice. Urinary collections were performed 24 h before the use of fluoridated dentifrice and 24 h (group A) or 48 h (group B) after. Fingernails were clipped every 2 weeks, for 26 weeks. Total F intake from diet and dentifrice was estimated. Fingernail F concentrations did not vary significantly throughout the study. Twenty-four-hour urinary F outputs (mean +/- SD, microg) were: 414 +/- 200 and 468 +/- 253 for placebo and F dentifrices, respectively (group A) and 402 +/-206, 691 +/- 345, 492 +/- 243 for placebo dentifrice, F dentifrice plus F varnish and F dentifrice, respectively (group B). The use of F dentifrice did not cause a significant increase in the urinary F output. However, when F varnish was used, a transitory increase in the urinary F output was detected (p = 0.001), returning to baseline levels in the last 24 h. Thus, F varnish is a safe method for topical F application even in children that use F dentifrice regularly. According to our protocol, urine was a suitable biomarker of exposure to F from dentifrice plus varnish, but not from dentifrice alone, while nails were not.