Background: The study was formulated to compare the efficacy of 38% SDF as a caries arresting agent as well as antibacterial and antiplaque agent in vivo with 5% sodium fluoride varnish (NaF) and 1.23% acidulated phosphate fluoride (APF) gel. Study Design: Total of 74 children aged 6-9 years (boys = 34, girls = 40) who had active caries with dmfs/DMFS score equal to or more than 1 were included in the study for a period of 12 months. Children were divided into three different groups-Group 1: 38%SDF Group 2: 5% fluoride varnish and Group 3: 1.23% APF gel. Fluoride application was done at baseline, 6th month and 12th month. Saliva collection was done at baseline, after 72 hrs, 6th month and12thmonth.Tryptone-yeastcysteine-sucrose-bacitracin agar (TYCSB) was used inoculate salivary Streptococcus mutans and incubated at 37°C for 72 hrs.The colony characteristics were studied and number of colony forming units of Streptococcus mutans (CFU/ml) of saliva were counted using digital colony counter.All subjects were evaluated for caries arrest status and plaque score (Silness&Loe index)at 6th and 12thmonthas well as Streptococcus mutans counts in saliva at 72 h, 6th and 12thmonth. Results: Significant reduction was found in caries arrest status plaque score as well as S. mutans counts in Group 1 as compared with Groups 2 and 3. Conclusion: In vivo application of SDF is effective in controlling progression of caries, decreases plaque score and S. mutans counts in saliva as compared to fluoride varnish and APF gel.