The aims of this present study were (1) to assess the antimicrobial effect of ozone from a novel ozone-generating device (Heolozone, USA) [0.052% (v/v) in air delivered at a rate of 13.33 ml.s(-1)] on primary root carious lesions (PRCLs) and (2) to evaluate the efficacy of ozone specifically on Streptococcus mutans and Streptococcus sobrinus. In study 1, 40 soft PRCLs from freshly extracted teeth were randomly divided into two groups to test the antimicrobial effect on PRCLs from exposure to ozonated water for either 10 or 20 s. Half of a lesion was removed using a sterile excavator. Subsequently, the remaining lesion was exposed to the ozonised water for a period of either 10 or 20 s (corresponding to 0. 069 or 0.138 ml of ozone, respectively). Using paired Student t tests, a significant (p<0.001) reduction (mean +/- SE) was observed in the ozone-treated groups with either a 10-second (log(10) 3.57+/-0.37) or 20-second (log(10) 3.77+/-0.42) ozone application compared with the control groups (log(10) 5.91+/-0.15 and log(10) 6.18+/-0.21, respectively). In study 2, 40 sterile saliva-coated glass beads were randomly divided into two groups for each micro-organism. One glass bead was put into each bijou bottle with 3 ml of Todd-Hewitt broth. S. mutans and S. sobrinus were inoculated anaerobically overnight. Each glass bead was then washed with 2 ml of phosphate-buffered saline. Immediately, 10 s of ozone gas was applied to each glass bead in the test groups. There was a significant (p<0.0001) reduction (mean +/- SE) in ozone-treated samples for S. mutans (log(10) 1.01+/-0.27) and S. sobrinus (log(10) 1.09+/-0.36) compared with the control samples (log(10) 3.93+/-0.07 and log(10) 4.61+/-0.13, respectively). This treatment regime is an effective, quick, conservative and simple method to kill micro-organisms in PRCLs. Ozone gas application for a period of 10 s was also capable of reducing the numbers of S. mutans and S. sobrinus on saliva-coated glass beads in vitro.