Highly alkaline environments induced by cement-based materials are likely to cause the physical and/or chemical properties of the bentonite buffer materials in radioactive waste repositories to deteriorate. Assessing long-term alteration of concrete/clay systems requires physicochemical models and a number of input parameters. In order to provide reliability in the assessment of the long-term performance of bentonite buffers under disposal conditions, it is necessary to develop and verify reactive transport codes for concrete/clay systems. In this study, a PHREEQC-based, reactive transport analysis code (MC-CEMENT ver. 2) was developed and was verified by comparing results of the calculations with in situ observations of the mineralogical evolution at the concrete/argillite interface. The calculation reproduced the observations such as the mineralogical changes in the argillite limited to within 1 cm in thickness from the interface, formation of CaCO3 and CSH, dissolution of quartz, decrease of porosity in the argillite and an increase in the concrete. These agreements indicate a possibility that models based on lab-scale (∼1 year) experiments can be applied to longer time scales although confidence in the models is necessary for much longer timescales. The fact that the calculations did not reproduce the dissolution of clays and the formation of gypsum indicates that there is still room for improvement in our model.