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 risk of dental fluorosis. This study investigated total daily fluoride intake (TDFI), excretion (TDFE) and retention (TDFR) in infants living in fluoridated and non-fluoridated water areas at pre- and post-weaning stages of development. Healthy infants, aged 0–12 months, were recruited and their TDFI (mg/kg body weight (BW) per d), from diet and toothpaste ingestion, was assessed over a 3-d period using a dietary diary and tooth-brushing questionnaire. TDFE (mg/kg BW per d) was estimated by collecting 48-h urine and faeces. TDFR (mg/kg BW per d) was estimated by subtracting TDFE from TDFI. A total of forty-seven infants completed the study: sixteen at pre-weaning and thirty-one at post-weaning stages, with a mean age of 3·4 and 10·0 months, respectively. TDFI was lower in the non-fluoridated area (P<0·001) and at the pre-weaning stage (P=0·002) but higher in formula-fed infants (P<0·001). TDFE was mainly affected by type of feeding, with higher excretion in formula-fed infants (P<0·001). TDFR was lower in the non-fluoridated area (P<0·001) and at the pre-weaning stage (P<0·001) but higher in formula-fed infants (P=0·001). In conclusion, a relatively large proportion of fluoride intake is retained in the body in weaned infants. This is an important consideration in fluoride-based prevention programmes, with goals to maximise caries prevention while minimising the risk of dental fluorosis.