The aim of this study was to evaluate the physical properties of calcium-silicate based cements as retrograde filling in different pH and blood conditions using micro-CT. Eighty-four teeth were obturated and after root-end resection, 3 mm-deep root-end cavity was ultrasonically prepared. The samples were divided into four test groups (n=21). Cements were freshly prepared and analyzed with micro-CT before and after exposed. The test groups were exposed for four days to environments containing acid, alkali, or blood. An acidic pH significantly reduced the volume of all materials after four days and differed from the other environments. Biodentine has the highest percentage of loss in volume and density after treatment in an acidic environment. Porosity formation in the acidic medium was observed in Biodentine amongst all materials. The three-dimensional structures of all materials changed after exposed to an acidic pH, while fewer changes were observed in the structures of materials treated with blood and alkali.