This in vitro study compared the ultrastructural quality of the apical seal achieved with Resilon/Epiphany and gutta-percha/AH Plus. Single-rooted extracted human teeth were prepared using a crown-down technique, debrided with NaOCl and EDTA, and obturated with either Resilon/Epiphany or gutta-percha/AH Plus. They were examined for gaps along canal walls using SEM, and for apical leakage using a transmission electron microscopy (TEM). SEM revealed both gap-free regions, and gap-containing regions in canals filled with both materials. TEM revealed the presence of silver deposits along the sealer-hybrid layer interface in Resilon/Epiphany, and between the sealer and gutta-percha in the controls. It is concluded that a complete hermetic apical seal cannot be achieved with either root filling materials.