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Purpose To compare the effect of the probiotic lozenges and chlorhexidine (CHX) mouthwash on plaque index (PI) , salivary pH and Streptococcus mutans (S. mutans) 3 count among groups of Saudi children. Methods A total of 54 participants aged 8-12 years were randomly allocated into three groups, 18 children in each group. Children in the probiotic group consumed one probiotic lozenge (Biogaia prodentis) daily, while children in the CHX group were instructed to use CHX mouthwash twice daily. The control group was only instructed to follow regular oral hygiene measures. Saliva samples were taken at baseline, 15th and 30th days. PI scores, salivary pH values and S. mutans count were evaluated. Data were statistically analyzed using the ANOVA and the Tukey post-hoc test. Results Probiotic lozenges and CHX mouthwash significantly reduced PI and S. mutans count and increased the salivary pH values. However, there were no statistical differences between the effect of probiotic lozenges and CHX mouthwash on PI (p-value= 800) and pH values (p-value= 0.927) on the 30th day. Conversely a significant difference was reported among their effects on S. mutans count (p-value=0.014) on the 30th day. Greater acceptance and compliance of children to probiotic lozenges were reported. Conclusions Probiotic lozenges could be an alternative to CHX mouthwash and encouraged to be included with the daily oral hygiene measures.