The aim of this study was to examine the changes in the cultivable microflora of carious dentin before and after atraumatic restorative treatment (ART) and investigate the inhibitory effect of chlorhexidine-gluconate-based cavity disinfectant in the microflora. Using a split mouth design, 35 primary molar pairs with class II carious lesions in 35 patients (mean age 7.31 +/- 0.47 years) were selected. The total viable counts (TVC), Streptococcus mutans and lactobacilli were first measured in the center of the infected demineralized lesion and then from the hard dentine after caries removal by the ART technique. Chlorhexidine-gluconate (2%)-based cavity disinfectant was applied to one of the molar pairs and the other molar received no disinfectant treatment. Thereafter, all of the teeth were restored with glass ionomer cement (GIC). Cavities were reassessed after 6 months and again dentine samples were microbiologically investigated. Removal of carious dentine by ART significantly reduced TVC, S. mutans and lactobacilli. After 6 months, application of chlorhexidine exhibited a greater significant reduction in TVC (p = 0.013), and a significant reduction in S. mutans compared to the nondisinfected group (p < 0.001). A significant reduction in lactobacilli counts was observed in both groups after 6 months, but the difference between the disinfected and nondisinfected groups was not significant (p = 0.056). ART was found to be effective in reducing the cultivable microflora and chlorhexidine-gluconate- based cavity disinfectant might serve as a suitable additional agent in inhibiting the residual bacteria in the dentine. Copyright (C) 2006 S. Karger AG, Basel.