Dental caries, caused by oral microbiota, is one of the most common human diseases. The present study aimed to investigate the effect of consumption of probiotic yogurt containing Bifidobacterium lactis Bb12 on salivary Streptococcus mutans and lactobacilli in students with initial stages of dental caries. In this double-blind randomized placebo-controlled clinical trial, 66 students (18–30 years) with initial stages of dental caries were selected and randomly assigned into 2 groups: the intervention group received 300 g/day of probiotic yogurt and the control group received 300 g/day of conventional yogurt for 2 weeks. An unstimulated fasting saliva sample was collected pre- and post-intervention. Bacterial counting was performed for salivary S. mutans and lactobacilli. A significant reduction in salivary S. mutans and lactobacillus counts was observed in the intervention group compared to their baseline and compared to the control group. In conclusion, it is suggested that the consumption of probiotic yogurt containing B. lactis Bb12 may modify the oral biofilm.