This study assessed the penetration of an epoxy resin-based sealer into dentinal tubules of root canals previously medicated with calcium hydroxide. Sixteen palatal root canals of upper molars were instrumented and distributed into two groups: (G1) root canals medicated with calcium hydroxide and obturated after its removal; (G2) root canals obturated without the use of dressing. Sealer mixed with rhodamine B provided fluorescence for confocal laser scanning microscopy. Measurements of area and linear penetration of the sealer were assessed in three thirds by ImageJ software. The data were statistically compared by Kruskal-Wallis, Dunn's and Mann-Whitney U tests (P < 0.01). The calcium hydroxide decreased the penetration of the sealer. The coronal and middle thirds had similar areas and linear penetrations in both groups, whereas the apical third had less penetration. In conclusion, the penetration of the epoxy resin-based sealer is influenced by the calcium hydroxide dressing used between appointments.