The aim of this study was to compare connective tissue and bacterial deposits on silicone sheets (SS) with expanded polytetrafluoroethylene membranes (ePTFE) used as barrier membranes in the guided tissue regeneration (GTR) for the periodontal treatment. Eighteen intrabony periodontal lesions from 18 patients were first surgically treated by GTR and either SS or ePTFE were used as barrier membranes. Four to 6 weeks after the first operation, membranes were retrieved from surgical sites and processed for the scanning electron microscopic study. Quantitative study of deposits on the lesion-facing surfaces of membranes was performed. The differences between the number of fields of connective tissue and bacteria on SS and ePTFE were analyzed by the Chi-square test at the level of 0.05 significance. The result showed no significant difference between the number of fields of connective tissue on the surfaces of SS and ePTFE (p=0.875). However, the number of fields of bacteria found on SS were significantly less than those found on ePTFE (p<0.001). The comparable number of fields of connective tissue deposits on both types of membranes suggests that the degree of healing under both types of membranes was also comparable. Therefore, SS can be used as a barrier membrane in the GTR for the periodontal treatment.