The aim of this study was to compare the efficacy of two preventive protocols -fluoride gel (F) alone or combined with chlorhexidine varnishes (CHX) - on sialochemical, clinical and microbiological parameters in a group of children at high cariogenic risk Two therapeutic-preventive protocols were applied in 73 children at high cariogenic risk (average age 6.2 +/- 1.4 years old) and clinical parameters (simplified oral hygiene index: OHI-S; decayed, missing and filled teeth: dmf index; sugar intake and exposure to fluoride), as well as sialochemical parameters (salivary pH and flow, buffer capacity) and microbiological parameters (CFU/mg of dental biofilm of Streptococcus mutans group) were recorded and correlated before and after the protocols. Association was found between parameters that cause deficient control of dental biofilm: high values of OHIS index, CFU/mg dental biofilm, sugar intake and the d component of dmft index, and lower values of salivary flow rate and buffer capacity. After the protocols, a significant decrease was found in OHI-S and CFU/mg dental biofilm. No significant difference was found with children's gender and age. The association observed between OHI-S and cariogenic bacteria emphasizes the importance of prevention, especially regarding the oral health of the most vulnerable children. The early inclusion of F associated with CHX in the initial step of preventive and therapeutic protocols would provide benefits regarding oral microbe control while children acquire new habits of oral hygiene.