To compare white ProRoot MTA (WMTA), EndoSequence BC sealer (BC sealer) and Biodentine with regard to their ability to produce apatites and cause Ca and Si incorporation in adjacent human root canal dentine after immersion in phosphate-buffered saline (PBS). Root sections of human single-rooted teeth were filled with one of the materials and immersed in PBS for 1, 7, 30 or 90 days (n = 5 each). Morphology and elemental composition of surface precipitates and interfacial dentine were analysed using a wavelength-dispersive X-ray spectroscopy electron probe microanalyser with image observation function. Ca- and Si-incorporation depths in the interfacial dentine were measured. In addition, the amount of Ca ions released from the test materials was measured by EDTA titration. All materials produced surface precipitates of acicular or lath-like morphology with Ca/P ratio of 1.6 : 2.0. Within dentinal tubules, the three materials formed tag-like structures that were frequently composed of Ca- and P-rich and Si-poor materials, suggesting intratubular precipitation. Ca- and Si-incorporation depths were in the order of Biodentine > WMTA > BC sealer, with a significant difference between BC sealer and the others at several time-points (P < 0.05, anova and Tukey's honestly significant difference test). The concentration of released Ca ions was in the order of Biodentine > WMTA > BC sealer with significant differences between the materials (P < 0.05). Compared with Biodentine and WMTA, BC sealer showed less Ca ion release and did not show Ca and Si incorporation as deeply in human root canal dentine when immersed in PBS for up to 90 days. © 2013 International Endodontic Journal. Published by John Wiley & Sons Ltd.