The oral cavity is a potential reservoir for respiratory pathogens. This longitudinal study investigated the association between upper respiratory tract infection (URI) and oral health among children. A total of 288 children aged 4 years were recruited. Their dental caries and oral hygiene status were clinically determined, using the dmft (decayed, missing and filled teeth) index and the Silness-Löe plaque index. Questionnaires were completed by parents to collect information on the child's socio-demographic background and URI episodes and symptoms in the following 12 months. Standard or zero-inflated negative binomial regressions were used to analyse the association between URI and both oral health indicators (dmft and plaque score). Some 138 (47.9%) children had URI in 12 months, including 63 (21.9%) and 75 (26.0%) children with 1-2 episodes and ≥3 episodes, respectively. The reported URI episodes fell into two peaks, coinciding with the two influenza peaks in Hong Kong. Significantly a higher dmft was found among children without URI compared with children who had ≥3 URI episodes (1.32 vs. 0.49; P = 0.043). The number of URI episodes was inversely associated with dmft (IRR = 0.851; 95% CI: 0.766-0.945; P = 0.003). There was no significant association between the plaque score and URI (P > 0.05). The children's caries experience was associated with reduced episodes of URI. Whether this inverse association is attributed to the immune response induced by dental caries is yet to be investigated.