Previous studies have shown that Self Arresting Caries Treatment (SACT) may be a useful technique to arrest active caries in Thai preschool children in remote areas. The objective of this study was to examine the effect of SACT on the levels of salivary mutans streptococci and lactobacilli in Thai children. Eighty-two subjects aged 4-6 years from primary school in a remote area of Thailand were recruited for this study. Each subject has at least two pairs of interproximal carious cavities between the first and second deciduous molars, and no history of severe pain. The subjects were divided into the control and SACT groups. The SACT technique was performed by removing food remnants and the surrounding overhang enamel of the carious cavity walls to enlarge the space between the carious cavities. The levels of mutans streptococci and lactobacilli in paraffin-stimulated whole saliva were determined at baseline, 2 and 4 months after treatment compared to those of the control group by the spatula method. The bacterial growth score was divided into three categories: 1 = 0-20 CFU, 2 = 21-100 CFU, and 3 > or = 100 CFU. At baseline, no differences in the mutans streptococci and lactobacilli scores were found between the SACT and control groups (p>0.05). Lower salivary lactobacilli levels were found in the SACT group on follow-up at 2 and 4 months (p<0.05), whereas the mutans streptococci level remained unchanged during these time periods. Our data confirms that the SACT technique can promote a self cleansing condition for interproximal lesions and can reduce the retentive sites in the oral cavity due to a reduction in salivary lactobacilli.