This study is aimed at determining whether a commercially available varnish, containing 40% chlorhexidine, is able to reduce the numbers of mutans streptococci and lactobacilli in saliva, in a moderately caries-active population in Surinam. 238 children, ages 13–14 years, were selected from different schools in Paramaribo, Surinam. From these children, total dental status was recorded and saliva samples were taken. At baseline and every 6 months, a 40% chlorhexidine varnish (EC40®) was applied. The control group received a neutral gel that did not contain chlorhexidine. The numbers of salivary mutans streptococci and lactobacilli were calculated by standard methods, and the caries status was recorded every 12 months. The study lasted 30 months. The results indicate that chlorhexidine varnish did not decrease the numbers of cariogenic bacteria, nor did it decrease caries progression. Moreover, in this population with a low dental health care, children with lactobacilli present in the saliva above our detection level, the chlorhexidine varnish even tended to increase caries progression, possibly due to selection of aciduric and acidogenic oral bacterial species. We therefore conclude that 40% chlorhexidine varnish is not likely to decrease caries in children in a high-treatment-need population without treatment of the sources of infection.