We aimed to compare the apical sealing ability of two experimental retrograde root-filling cements and mineral trioxide aggregate using a fluid filtration method. X-ray diffraction (XRD) and X-ray fluorescence spectrometry (XRF) were used to evaluate structural and qualitative characteristics. Thirty single-rooted extracted teeth were treated, root-end prepared, and obturated using MTA and two experimental cements. Fluid filtration was measured during a 5-minute period after 4, 24, and 48 hours and 1, 2, and 12 weeks. The results were statistically compared by using a two-way analysis of variance (p < 0.05). The marginal adaptation was evaluated by using a SEM replica technique. XRD analyses showed similar patterns. XRF showed lower amounts of SiO(2) and FeO(3) in the experimental cements. All cements showed a reduced fluid flow rate over time. No significant differences were found between the cements. The SEM replica indicated a good marginal adaptation to dentinal walls. Both experimental cements showed suitable properties as retrograde root-filling materials.