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Caries infiltration aims to inhibit lesion progression, by occluding the porosities within the lesion body with low-viscosity resins. The ability in hampering lesion progression is correlated with the penetration depth (PD) of the infiltrant.This study aimed to compare the infiltration depths into proximal lesions in primary molars after different application times.Noncavitated natural caries lesions (n = 83) were etched with 15% HCl for 2 min and infiltrated for 0.5, 1, 3, or 5 min. Specimens were sectioned and PD at the maximum lesion depth (LDmax) were analysed using dual fluorescence confocal microscopy.Percentage penetrations (PD/LDmax) were significantly higher after 3 or 5 min compared with 0.5-min application (P < 0.05; Mann–Whitney test). For LDmax <400 μm, no significant differences were observed between application times (P > 0.05). For LDmax≥400 μm, 3- and 5-min application resulted in significantly deeper infiltration compared with 0.5 min (P < 0.05). After 1-min application, PD was significantly lower than 5 min (P < 0.05), PD/LDmax did not differ from all other groups (P > 0.05).Natural noncavitated proximal lesions in primary molars were deeply infiltrated after 1-min application in vitro. For deeper lesions, however, more consistent results were obtained after 3 min.