BackgroundMature teeth with chronic apical abscesses characterized by intermittent discharge of pus through an associated sinus tract. This communication between oral mucosa and periapical inflammation is challenging for the sealing ability of root canal obturation material. Therefore, the study aim was to compare the outcomes of endodontic treatment using mineral trioxide aggregate (MTA) cement to the conventional gutta-percha cone and root canal sealer as an obturation material in mature teeth with chronic apical abscesses.MethodsMature teeth with chronic apical abscesses referred to our clinic for root canal treatment between 2010 and 2012 were treated in a single visit and distributed among treatment (T) and control (C) groups using a predetermined randomization block (TCTC). After chemo-mechanical preparation, teeth in group T received MTA cement mixed in a 0.26 water to powder ratio, and teeth group C received gutta-percha and root canal sealer using the warm vertical technique. The treatment outcomes were defined as obturation length, periapical healing, resorption of extruded material, and survival rate at least 2.5 years after treatment. Three endodontists blinded to the type of obturation material documented treatment outcomes. Statistical analysis at P < 0.05 was conducted to measure difference between the groups.ResultsThirty-six teeth were treated between 2010 and 2012, and 32 teeth were evaluated in 2015. Complete periapical healing was observed in 87.5 % of MTA-treated teeth and 75.0 % of gutta-percha-treated teeth. Adequate obturation length was reported in 50.0 % of MTA-treated and 37.5 % of gutta-percha-treated teeth. Complete resorption of extruded material was evident in 83.3 % MTA-treated teeth and 100.0 % gutta-percha-treated teeth. The survival rate of MTA-treated teeth was 100 % at 3, and 5 years, while the survival rate of gutta-percha-treated teeth was 83.3 % at 3, and 5 years. There was no significant difference between the groups in term of periapical healing, survival rate, obturation length, or resorption of extruded material.ConclusionsThe outcomes of single-visit endodontic treatment of mature teeth with chronic apical abscesses using MTA cement were better, but not statistically significant, compared to conventional treatment.Trial registrationISRCTN15285974. Registered retrospectively 23 June 2015.Electronic supplementary materialThe online version of this article (doi:10.1186/s12903-016-0276-y) contains supplementary material, which is available to authorized users.