Limited knowledge is available on total fluoride exposure, excretion and retention in infants, despite the first year of human life being the critical period for dental development and the risk of dental fluorosis. In this observational study, we measured 1) total fluoride intake, from diet and toothpaste ingestion, using a dietary-diary and a toothbrushing-questionnaire; 2) total fluoride excretion by collecting 48h urine and faeces; and 3) body fluoride retention subtracting intake from excretion. Our results showed that a relatively large proportion of fluoride intake is retained in the body (i.e. deposited in calcifying tissues) in weaned formula-fed infants. This is an important consideration in fluoride-based prevention programmes with goals to maximise caries prevention while minimising dental fluorosis risk.