Purpose: To evaluate the effects of fluoride varnish vs a combination of chlorhexidine-thymol varnish plus a gel containing chlorhexidine and fluoride on oral hygiene and caries prevention in disabled children. Materials and Methods: Ninety patients aged 3-17 years who were treated under general anaesthesia were randomly assigned into three groups as follows: group 1: Fluor Protector (0.1% fluoride varnish); group 2: Cervitec Plus (1% chlorhexidine- 1% thymol varnish) + Cervitec Gel (0.2% chlorhexidine-0.2% sodium fluoride); group 3: control (toothbrushing only). Mutans streptococci (MS) and lactobacilli (LB) levels, visible plaque index (VPI) and gingival bleeding index (GBI) were evaluated at four stages: T0, before general anaesthesia; T1, one month after treatment; T2, six months after treatment; T3, twelve months after treatment. The data were evaluated using Kruskal-Wallis and Mann-Whitney U-tests (P 0.05). Results: Groups 1 and 2 showed significantly lower scores than group 3 for all parameters at T1 and T2. No statistically significant difference was detected among any of the the groups at T3 (P > 0.05). Conclusion: The use of materials that include both fluoride and chlorhexidine as routine treatment of children with disability may increase the success of restorations by improving oral hygiene, reduce the need for future restorative treatments and thus the need for general anaesthesia. Keywords: antibacterial effect, children with disability, chlorhexidine, fluoride, general anaesthesia