There has been no comparison between fluoride concentrations in urine and nails of children exposed to different sources of systemic fluoride. The aim of this study was to compare the relationship between fluoride intake with urinary fluoride excretion and fluoride concentrations in fingernails and toenails of children receiving fluoride from artificially fluoridated water (0.6-0.8 mg F/L, n = 25), naturally fluoridated water (0.6-0.9 mg F/L, n = 21), fluoridated salt (180-200 mg F/Kg, n = 26), and fluoridated milk (0.25 mg F, n = 25). A control population was included (no systemic fluoride, n = 24). Fluoride intake from diet and dentifrice, urinary fluoride excretion, and fluoride concentrations in fingernails/toenails were evaluated. Fluoride was analyzed with an ion-selective electrode. Urinary fluoride excretion in the control community was significantly lower when compared with that in the fluoridated cities, except for the naturally fluoridated community. However, the same pattern was not as evident for nails. Both urinary fluoride output and fluoride concentrations in fingernails/toenails were significantly correlated to total fluoride intake. However, the correlation coefficients for fluoride intake and urinary fluoride output were lower (r = 0.28, p < 0.01) than those observed for fingernails/toenails (r = 0.36, p < 0.001), suggesting that nails might be slightly better indicators of fluoride intake at the individual level.