Sealing compound is used at the joints of stone cladding for waterproofing requirements. However, dark discoloration and pattern staining of the joint area have been occurring. Therefore, this research was made to quantitatively evaluate the effects on the joint area of sealing compound type, joint direction, and stain removal by cleaning to make the staining problem clear. The following information was obtained : i. Adequate evaluation of staining due to sealing compound was made by measurements of color differences and glossiness of stone and microscopic observation of undesirable substance on stone. It was quantitatively confirmed that compared to other sealing compounds, silicone based sealing compound caused staining remarkably. ii. Staining of stone due to silicone based sealing compound was prominent in the area below horizontal joints and silicone oil propagation on the stone surface was of a more dominant transfer mechanism than diffusion. iii. Decrease in color differences and increase in glossiness due to cleaning were noted confirming staining removal effect but tendency for increased staining due to exposure after cleaning was observed. The reason for this was that the stone surface was newly exposed due to cleaning. The knowledge and findings obtained in this research are essential information for the quality of stone work.