Ca(OH)2 aqueous slurry is widely used as an inter-appointment antimicrobial dressing in root canal treatment. The aim of this study was to quantify the particle size and shape of commercial-grade UltraCal XS (UC) and to compare it with that of research-grade Ca(OH)2 (RG) using a flow particle image analyzer (FPIA). The morphology and penetration inside the dentin tubules of the UC and RG particles were examined using a scanning electron microscope (SEM). UC and RG (10 mg) were mixed with 15 mL of alcohol, and were sonicated. Five milliliters of the dispersion was subjected to FPIA, and particle length, width, perimeter and aspect ratio were analyzed. In addition, UC paste and RG aqueous slurry were agitated on dentin discs and were prepared for SEM examination. There were significant differences between UC and RG with regard to the frequency of different length groups (P < 0.0001). UC contained smaller particles than RG (P < 0.0001). Under SEM, the agitated UC and RG particles occluded the opening of dentin tubules and penetrated inside the dentin tubules. The size of UC particles is smaller than those of RG. Both UC and RG particles were able to penetrate into open dentin tubules.