Aims and Objectives: to evaluate the antibacterial action of calcium silicate (Theracal) liner in comparison to calcium hydroxide (Biner LC) liners on permanent carious molars treated with step-wise excavation in 6 months follow-up. Materials and Methods:48 patients were assigned in this study. Participants were divided into two groups randomly according to type of liner that was placed and sample of dentin that will be taken before placement of liner and after placement 6 months. Application of both materials was done after the excavation of caries on the cavity walls and dentin sample was taken from the central carious lesion for microbiological analysis, cavities were sealed with conventional glass ionomer cement as a temporary restoration. After 6 months, the cavities were reopened, temporary restorations and pulp capping material were removed, and second dentin sample was taken for microbiological analysis. Caries was excavated to firm dentin and teeth were restored with permanent resin composite restorations. Agar Diffusion test and Digital Colony Counter were conducted for the study. The measuring unit of the bacterial count was CFU/ml. Results: There was no statistically significant difference between the two groups for Streptococcus Mutants and Lactobacillus Bacterial count after 6 months. Conclusion: Antibacterial activity of the resin-modified calcium silicate has nearly the same effect as Calcium Hydroxide, however still doubtful to be used as the gold standard for pulp capping material. Regardless the pulp capping material used, avoiding bacterial contamination and marginal sealing is essential in preserving the tooth vitality with deep Class I carious lesions.